diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md index 8944d4511..c91f6b310 100644 --- a/reports/anvil-edge/README.md +++ b/reports/anvil-edge/README.md @@ -13,4 +13,4 @@ After each successful deployment, automated tool tests are also run against the Latest tool tests for each chunk: -
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 02 06:26:43 2024Mon Aug 26 06:26:05 2024
1ToolsetMon Sep 02 18:31:49 2024Mon Aug 26 18:31:46 2024
2ToolsetTue Aug 27 06:26:39 2024Tue Aug 20 06:25:04 2024
3ToolsetTue Aug 27 18:39:36 2024Tue Aug 20 18:31:06 2024
4ToolsetWed Aug 28 06:26:28 2024Wed Aug 21 06:25:47 2024
5ToolsetWed Aug 21 18:31:30 2024Wed Aug 14 18:31:52 2024
6ToolsetThu Aug 29 06:25:45 2024Thu Aug 22 06:25:48 2024
7ToolsetThu Aug 29 18:32:00 2024Thu Aug 22 18:43:08 2024
8ToolsetFri Aug 30 06:25:36 2024Fri Aug 23 06:25:56 2024
9ToolsetFri Aug 30 18:31:41 2024Fri Aug 23 18:38:12 2024
10ToolsetSat Aug 31 06:24:40 2024Sat Aug 24 06:23:31 2024
11ToolsetSat Aug 31 18:29:37 2024Sat Aug 24 18:29:36 2024
12ToolsetSun Sep 01 06:26:20 2024Sun Aug 25 06:24:42 2024
13ToolsetSun Sep 01 18:29:57 2024Sun Aug 25 18:29:56 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 02 06:26:43 2024Mon Aug 26 06:26:05 2024
1ToolsetMon Sep 02 18:31:49 2024Mon Aug 26 18:31:46 2024
2ToolsetTue Sep 03 06:25:36 2024Tue Aug 27 06:26:39 2024
3ToolsetTue Aug 27 18:39:36 2024Tue Aug 20 18:31:06 2024
4ToolsetWed Aug 28 06:26:28 2024Wed Aug 21 06:25:47 2024
5ToolsetWed Aug 21 18:31:30 2024Wed Aug 14 18:31:52 2024
6ToolsetThu Aug 29 06:25:45 2024Thu Aug 22 06:25:48 2024
7ToolsetThu Aug 29 18:32:00 2024Thu Aug 22 18:43:08 2024
8ToolsetFri Aug 30 06:25:36 2024Fri Aug 23 06:25:56 2024
9ToolsetFri Aug 30 18:31:41 2024Fri Aug 23 18:38:12 2024
10ToolsetSat Aug 31 06:24:40 2024Sat Aug 24 06:23:31 2024
11ToolsetSat Aug 31 18:29:37 2024Sat Aug 24 18:29:36 2024
12ToolsetSun Sep 01 06:26:20 2024Sun Aug 25 06:24:42 2024
13ToolsetSun Sep 01 18:29:57 2024Sun Aug 25 18:29:56 2024
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json index 78ecee064..d28012c94 100644 --- a/reports/anvil-edge/tool-tests/chunks.json +++ b/reports/anvil-edge/tool-tests/chunks.json @@ -7,11 +7,11 @@ "date2": "Mon Aug 26 18:31:46 2024" }, "2": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-27-06-11-1/results.html", - "date1": "Tue Aug 27 06:26:39 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-27-06-11-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-20-06-10-1/results.html", - "date2": "Tue Aug 20 06:25:04 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/results.html", + "date1": "Tue Sep 03 06:25:36 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-27-06-11-1/results.html", + "date2": "Tue Aug 27 06:26:39 2024" }, "3": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-27-18-16-1/results.html", diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/chunk.json new file mode 100644 index 000000000..c794c8d95 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/chunk.json @@ -0,0 +1,7 @@ +{ + "2": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/results.html", + "date1": "Tue Sep 03 06:25:36 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/chunk.txt new file mode 100644 index 000000000..a97d54fcc --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/chunk.txt @@ -0,0 +1,20 @@ +-t miniasm --tool-version 8dee0218ac7d +-t deeptools_bigwig_compare --tool-version 26e7304d6737 +-t fastq_groomer --tool-version 47e5dbc3e790 +-t sra_tools --tool-version 83c7d564b128 +-t mummer_mummerplot --tool-version ebe3b0f84de9 +-t poretools_qualpos --tool-version 4fe6b96aff72 +-t kallisto_pseudo --tool-version 5ae5c312d718 +-t sam_pileup --tool-version a3b4ad6858ff +-t samtools_calmd --tool-version 06dc50b7b711 +-t music_manipulate_eset --tool-version 22232092be53 +-t droplet_barcode_plot --tool-version 8f605643ccfd +-t scater_plot_exprs_freq --tool-version 058b40656107 +-t scanpy_parameter_iterator --tool-version 0387a2179f88 +-t query_tabular --tool-version cf34c344508d +-t column_remove_by_header --tool-version 372967836e98 +-t snpsift --tool-version 2e497a770bca +-t bcftools_plugin_mendelian --tool-version bf235558f2cf +-t bcftools_csq --tool-version fdd127bd4a32 +-t vcfcommonsamples --tool-version f1852ecef841 +-t vcfdistance --tool-version c506b8275b1a diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/101b56dd69096d11.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/101b56dd69096d11.json new file mode 100644 index 000000000..30761d516 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/101b56dd69096d11.json @@ -0,0 +1,101 @@ +{ + "model_class": "Job", + "id": "101b56dd69096d11", + "history_id": "c5fe43971bba42f1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3", + "state": "error", + "exit_code": 127, + "create_time": "2024-09-03T06:52:31.325977", + "update_time": "2024-09-03T06:52:46.150783", + "galaxy_version": "24.1", + "external_id": "gxy-kc4wx", + "handler": null, + "job_runner_name": null, + "command_line": "ln -s '/galaxy/server/database/objects/0/6/5/dataset_06523432-b9d1-4891-b7d3-e4f400182d1f.dat' input1.bam && ln -s '/galaxy/server/database/objects/_metadata_files/8/5/3/metadata_853b3ca5-b2b1-4b83-8363-91890d787490.dat' 'input1.bam.bai' && ln -s '/galaxy/server/database/objects/3/b/b/dataset_3bb2da50-e1ca-44ce-a322-d63f5df29347.dat' reference.fasta && samtools faidx reference.fasta && samtools pileup -M 60 -f reference.fasta input1.bam > '/galaxy/server/database/objects/6/e/a/dataset_6eae9bca-de3a-49f3-a1fe-3848034e3fd9.dat'", + "user_email": "tests@fake.org", + "command_version": "", + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"equCab2\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/equCab2.len\"", + "c": "{\"__current_case__\": 0, \"consensus\": \"no\"}", + "mapCap": "\"60\"", + "indels": "\"no\"", + "lastCol": "\"no\"", + "refOrHistory": "{\"__current_case__\": 1, \"input1\": {\"values\": [{\"id\": 127, \"src\": \"hda\"}]}, \"ownFile\": {\"values\": [{\"id\": 128, \"src\": \"hda\"}]}, \"reference\": \"history\"}" + }, + "inputs": { + "refOrHistory|input1": { + "id": "519c268d6e571334", + "src": "hda", + "uuid": "06523432-b9d1-4891-b7d3-e4f400182d1f" + }, + "refOrHistory|ownFile": { + "id": "f9ab1f8db539c4c2", + "src": "hda", + "uuid": "3bb2da50-e1ca-44ce-a322-d63f5df29347" + } + }, + "outputs": { + "output1": { + "id": "156ba8706e2576b1", + "src": "hda", + "uuid": "6eae9bca-de3a-49f3-a1fe-3848034e3fd9" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory\n", + "job_stdout": "", + "job_stderr": "", + "stdout": "", + "stderr": "samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory\n", + "job_messages": [ + { + "code_desc": "", + "desc": "Fatal error: Exit code 127 ()", + "error_level": 3, + "exit_code": 127, + "type": "exit_code" + } + ], + "dependencies": [], + "job_metrics": [ + { + "title": "Job Runtime (Wall Clock)", + "value": "0 seconds", + "plugin": "core", + "name": "runtime_seconds", + "raw_value": "0E-7" + }, + { + "title": "Job End Time", + "value": "2024-09-03 06:52:35", + "plugin": "core", + "name": "end_epoch", + "raw_value": "1725346355.0000000" + }, + { + "title": "Job Start Time", + "value": "2024-09-03 06:52:35", + "plugin": "core", + "name": "start_epoch", + "raw_value": "1725346355.0000000" + }, + { + "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" + } + ] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/60dc8ed2ca8581ac.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/60dc8ed2ca8581ac.json new file mode 100644 index 000000000..90da0e94b --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/60dc8ed2ca8581ac.json @@ -0,0 +1,60 @@ +{ + "model_class": "Job", + "id": "60dc8ed2ca8581ac", + "history_id": "c5fe43971bba42f1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", + "state": "error", + "exit_code": null, + "create_time": "2024-09-03T06:58:10.264162", + "update_time": "2024-09-03T06:58:14.627333", + "galaxy_version": "24.1", + "external_id": "gxy-44j2j", + "handler": null, + "job_runner_name": null, + "command_line": "cat '/galaxy/server/database/jobs_directory/000/130/configs/tmp7_jrxnls' && cp '/galaxy/server/database/objects/e/1/0/dataset_e106e609-955c-4b07-8741-017cc91a020e.dat' 'workdb.sqlite' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/130/configs/tmpy5o6f8gl' -Q '/galaxy/server/database/jobs_directory/000/130/configs/tmp7_jrxnls' --comment_char='#' -o '/galaxy/server/database/objects/8/c/8/dataset_8c882cff-dcfc-4326-b285-ddc57cecc7db.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"sqlite\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "addqueries": "{\"queries\": []}", + "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", + "sqlquery": "\"SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\"", + "save_db": "false", + "modify_database": "{\"sql_stmts\": []}", + "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"^\\\\d+\"}}, {\"__index__\": 1, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}, {\"__index__\": 2, \"filter\": {\"__current_case__\": 3, \"filter_type\": \"append_line_num\"}}, {\"__index__\": 3, \"filter\": {\"__current_case__\": 9, \"columns\": \"7,2,3,4,1\", \"filter_type\": \"select_columns\"}}, {\"__index__\": 4, \"filter\": {\"__current_case__\": 11, \"add\": null, \"column\": \"c4\", \"filter_type\": \"replace\", \"regex_pattern\": \"(\\\\d+)/(\\\\d+)/(\\\\d+)\", \"regex_replace\": \"19\\\\3-\\\\2-\\\\1\"}}]}, \"table\": {\"values\": [{\"id\": 153, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"id,first,last,dob,pets\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"people\"}}]", + "add_to_database": "{\"withdb\": {\"values\": [{\"id\": 152, \"src\": \"hda\"}]}}", + "workdb": "\"workdb.sqlite\"" + }, + "inputs": { + "add_to_database|withdb": { + "id": "5cfa2c742a69011a", + "src": "hda", + "uuid": "e106e609-955c-4b07-8741-017cc91a020e" + }, + "tables_0|table": { + "id": "b17c5c82cd3ecfce", + "src": "hda", + "uuid": "b746cd5b-f442-4c12-9a2d-08f780790990" + } + }, + "outputs": { + "output": { + "id": "ac7f57a7a56a19b0", + "src": "hda", + "uuid": "8c882cff-dcfc-4326-b285-ddc57cecc7db" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "\nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n ", + "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/b/7/4/dataset_b746cd5b-f442-4c12-9a2d-08f780790990.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}]}\n\nSQL: \nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n \nrowcount: None\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "\nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n ", + "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/b/7/4/dataset_b746cd5b-f442-4c12-9a2d-08f780790990.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}]}\n\nSQL: \nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n \nrowcount: None\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/95e5dec2fbf26496.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/95e5dec2fbf26496.json new file mode 100644 index 000000000..1f5806503 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/95e5dec2fbf26496.json @@ -0,0 +1,49 @@ +{ + "model_class": "Job", + "id": "95e5dec2fbf26496", + "history_id": "c5fe43971bba42f1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", + "state": "error", + "exit_code": null, + "create_time": "2024-09-03T06:46:14.137222", + "update_time": "2024-09-03T06:46:19.068042", + "galaxy_version": "24.1", + "external_id": "gxy-7l5xz", + "handler": null, + "job_runner_name": null, + "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/4/6/2/dataset_46264658-3f70-4f21-8bc4-767b9965501a.dat' sanger.gz '/galaxy/server/database/objects/0/2/c/dataset_02ce87b3-3454-4ad3-83df-7d3fd4f7d3f5.dat' sanger ascii summarize_input", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"fastq.gz\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", + "input_type": "\"sanger\"" + }, + "inputs": { + "input_file": { + "id": "6f9ddc11486f4483", + "src": "hda", + "uuid": "46264658-3f70-4f21-8bc4-767b9965501a" + } + }, + "outputs": { + "output_file": { + "id": "95e5dec2fbf26496", + "src": "hda", + "uuid": "02ce87b3-3454-4ad3-83df-7d3fd4f7d3f5" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "Groomed 2 sanger.gz reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "Groomed 2 sanger.gz reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/98623284f686bc7c.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/98623284f686bc7c.json new file mode 100644 index 000000000..559397a7e --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/98623284f686bc7c.json @@ -0,0 +1,60 @@ +{ + "model_class": "Job", + "id": "98623284f686bc7c", + "history_id": "c5fe43971bba42f1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", + "state": "error", + "exit_code": null, + "create_time": "2024-09-03T06:59:45.209611", + "update_time": "2024-09-03T06:59:49.873153", + "galaxy_version": "24.1", + "external_id": "gxy-mpbcg", + "handler": null, + "job_runner_name": null, + "command_line": "cat '/galaxy/server/database/jobs_directory/000/137/configs/tmpljwbu6nc' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/137/configs/tmpmsqj69lx' -Q '/galaxy/server/database/jobs_directory/000/137/configs/tmpljwbu6nc' --comment_char='#' -o '/galaxy/server/database/objects/6/0/d/dataset_60da0121-d131-4f09-8906-54a9df5c81a7.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"tabular\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "addqueries": "{\"queries\": [{\"__index__\": 0, \"query_result\": {\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}, \"sqlquery\": \"SELECT * FROM psms WHERE confidence > 97.0\"}]}", + "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", + "sqlquery": "\"SELECT scan,\\\"m/z\\\", \\\"Precursor m/z Error [ppm]\\\", Sequence, \\\"Protein(s)\\\", confidence FROM PSMs WHERE NOT re_search(', ',\\\"Protein(s)\\\")\"", + "save_db": "false", + "modify_database": "{\"sql_stmts\": [{\"__index__\": 0, \"sqlstmt\": \"UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0\"}]}", + "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 9, \"columns\": \"1,3,2,6,14,19,23\", \"filter_type\": \"select_columns\"}}]}, \"table\": {\"values\": [{\"id\": 160, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"scan,,,,,,confidence\", \"column_names_from_first_line\": true, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"PSMs\"}}]", + "add_to_database": "{\"withdb\": null}", + "workdb": "\"workdb.sqlite\"" + }, + "inputs": { + "tables_0|table": { + "id": "f88cf8ee998749f2", + "src": "hda", + "uuid": "06d6bda3-00a4-44af-bf95-4105b34dca77" + } + }, + "outputs": { + "output": { + "id": "4306367a50dd42eb", + "src": "hda", + "uuid": "60da0121-d131-4f09-8906-54a9df5c81a7" + }, + "output1": { + "id": "287c916884dcddd5", + "src": "hda", + "uuid": "af560828-98a1-4e90-a79c-bb812ced1a2b" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "\nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n ", + "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/0/6/d/dataset_06d6bda3-00a4-44af-bf95-4105b34dca77.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'scan,,,,,,confidence', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19, 23]}]}], 'sql_stmts': ['UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0'], 'queries': [{'query': 'SELECT * FROM psms WHERE confidence > 97.0', 'result_file': 'results0.tsv', 'header': ''}]}\n\nDB modification: UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0 \nrowcount: \n\nSQL: SELECT * FROM psms WHERE confidence > 97.0 \nrowcount: None\n\nSQL: \nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n \nrowcount: None\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "\nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n ", + "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/0/6/d/dataset_06d6bda3-00a4-44af-bf95-4105b34dca77.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'scan,,,,,,confidence', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19, 23]}]}], 'sql_stmts': ['UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0'], 'queries': [{'query': 'SELECT * FROM psms WHERE confidence > 97.0', 'result_file': 'results0.tsv', 'header': ''}]}\n\nDB modification: UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0 \nrowcount: \n\nSQL: SELECT * FROM psms WHERE confidence > 97.0 \nrowcount: None\n\nSQL: \nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n \nrowcount: None\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/ac7f57a7a56a19b0.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/ac7f57a7a56a19b0.json new file mode 100644 index 000000000..ee7abd067 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/ac7f57a7a56a19b0.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "ac7f57a7a56a19b0", + "history_id": "c5fe43971bba42f1", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-03T07:03:43.155944", + "update_time": "2024-09-03T07:03:53.617492", + "galaxy_version": "24.1", + "external_id": "gxy-b94px", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/154/registry.xml' '/galaxy/server/database/jobs_directory/000/154/upload_params.json' '179:/galaxy/server/database/objects/4/a/8/dataset_4a81b91a-586b-45ac-95a1-36ddcfd6e421_files:/galaxy/server/database/objects/4/a/8/dataset_4a81b91a-586b-45ac-95a1-36ddcfd6e421.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_n9wy7_9o\"", + "files_metadata": "{\"__current_case__\": 99, \"file_type\": \"gff3\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"csq.gff3\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_k2tnih3t\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"gff3\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "7c64a83d092efbd8", + "src": "hda", + "uuid": "4a81b91a-586b-45ac-95a1-36ddcfd6e421" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/b00016d73b432039.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/b00016d73b432039.json new file mode 100644 index 000000000..998d86d03 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/b00016d73b432039.json @@ -0,0 +1,49 @@ +{ + "model_class": "Job", + "id": "b00016d73b432039", + "history_id": "c5fe43971bba42f1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", + "state": "error", + "exit_code": null, + "create_time": "2024-09-03T06:31:17.352129", + "update_time": "2024-09-03T06:31:23.310575", + "galaxy_version": "24.1", + "external_id": "gxy-cskwz", + "handler": null, + "job_runner_name": null, + "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/9/4/f/dataset_94fee34c-4103-4f79-9dba-cfe66412a7e1.dat' sanger '/galaxy/server/database/objects/4/d/1/dataset_4d10b5a3-867a-4461-8959-3ba23cee6a17.dat' sanger ascii summarize_input", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"fastq\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", + "input_type": "\"sanger\"" + }, + "inputs": { + "input_file": { + "id": "e9f7c7443e767705", + "src": "hda", + "uuid": "94fee34c-4103-4f79-9dba-cfe66412a7e1" + } + }, + "outputs": { + "output_file": { + "id": "b00016d73b432039", + "src": "hda", + "uuid": "4d10b5a3-867a-4461-8959-3ba23cee6a17" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/db8ee8927138dbc6.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/db8ee8927138dbc6.json new file mode 100644 index 000000000..f22c918d4 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/db8ee8927138dbc6.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "db8ee8927138dbc6", + "history_id": "c5fe43971bba42f1", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-03T06:59:17.229373", + "update_time": "2024-09-03T06:59:27.564655", + "galaxy_version": "24.1", + "external_id": "gxy-hcrpq", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/135/registry.xml' '/galaxy/server/database/jobs_directory/000/135/upload_params.json' '159:/galaxy/server/database/objects/0/6/7/dataset_067f95a7-2059-4664-b6d2-3a092ef4cc7c_files:/galaxy/server/database/objects/0/6/7/dataset_067f95a7-2059-4664-b6d2-3a092ef4cc7c.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_tieju0sk\"", + "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"psm_report.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_f4ea25io\", \"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": "4b02a6855a4b807b", + "src": "hda", + "uuid": "067f95a7-2059-4664-b6d2-3a092ef4cc7c" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/ddf248f53d379e98.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/ddf248f53d379e98.json new file mode 100644 index 000000000..eae940953 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/ddf248f53d379e98.json @@ -0,0 +1,49 @@ +{ + "model_class": "Job", + "id": "ddf248f53d379e98", + "history_id": "c5fe43971bba42f1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", + "state": "error", + "exit_code": null, + "create_time": "2024-09-03T06:37:02.748681", + "update_time": "2024-09-03T06:37:07.586421", + "galaxy_version": "24.1", + "external_id": "gxy-t4bpr", + "handler": null, + "job_runner_name": null, + "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/f/0/1/dataset_f0152540-eb17-448a-bec0-ec271eb6e040.dat' sanger '/galaxy/server/database/objects/a/c/d/dataset_acd596b8-ccd3-45ec-a066-a9ae826baad5.dat' cssanger None summarize_input --fix-id", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"fastq\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"cssanger\", \"summarize_input\": \"summarize_input\"}", + "input_type": "\"sanger\"" + }, + "inputs": { + "input_file": { + "id": "04be3fcc63c7ff40", + "src": "hda", + "uuid": "f0152540-eb17-448a-bec0-ec271eb6e040" + } + }, + "outputs": { + "output_file": { + "id": "ddf248f53d379e98", + "src": "hda", + "uuid": "acd596b8-ccd3-45ec-a066-a9ae826baad5" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "Groomed 2 sanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "Groomed 2 sanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/e568629811fc8172.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/e568629811fc8172.json new file mode 100644 index 000000000..d08b69f45 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/e568629811fc8172.json @@ -0,0 +1,85 @@ +{ + "model_class": "Job", + "id": "e568629811fc8172", + "history_id": "c5fe43971bba42f1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", + "state": "error", + "exit_code": 1, + "create_time": "2024-09-03T06:30:45.681757", + "update_time": "2024-09-03T06:30:58.809528", + "galaxy_version": "24.1", + "external_id": "gxy-wqm8m", + "handler": null, + "job_runner_name": null, + "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/3/4/4/dataset_3443d596-7865-4b06-a918-b42375674ca6.dat' sanger '/galaxy/server/database/objects/f/d/3/dataset_fd35fc07-8dea-4bb5-b485-7bf007537abc.dat' sanger ascii summarize_input --no-fix-id", + "user_email": "tests@fake.org", + "command_version": "", + "params": { + "__input_ext": "\"fastq\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "options_type": "{\"__current_case__\": 1, \"fix_id\": false, \"force_quality_encoding\": \"ascii\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", + "input_type": "\"sanger\"" + }, + "inputs": { + "input_file": { + "id": "02710b4481840932", + "src": "hda", + "uuid": "3443d596-7865-4b06-a918-b42375674ca6" + } + }, + "outputs": { + "output_file": { + "id": "e568629811fc8172", + "src": "hda", + "uuid": "fd35fc07-8dea-4bb5-b485-7bf007537abc" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "There was an error reading your input file. Your input file is likely malformed.\nIt is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below.\nHowever, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism.\n\nThe reported error is: 'Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).'.\nThe error occurred at the start of your file and no valid FASTQ reads were found.\nThe error in your file occurs between lines '1' and '3', which corresponds to byte-offsets '0' and '33', and contains the text (33 of 33 bytes shown):\n\n@FAKE-1\nACGTACGTAC\n+invalid line\n\n", + "tool_stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/gx-fastq-groomer\", line 10, in \n sys.exit(main())\n ^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 99, in main\n Groomer().run()\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 48, in run\n for read_count, fastq_read in enumerate(reader):\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 683, in __iter__\n yield next(self)\n ^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 742, in __next__\n raise e\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 724, in __next__\n block = super(fastqVerboseErrorReader, self).__next__()\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 621, in __next__\n self._read_fastq_sequence(rval, id_line)\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 666, in _read_fastq_sequence\n raise fastqFormatError(\ngalaxy_utils.sequence.fastq.fastqFormatError: Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).\n", + "job_stdout": "", + "job_stderr": "", + "stdout": "There was an error reading your input file. Your input file is likely malformed.\nIt is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below.\nHowever, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism.\n\nThe reported error is: 'Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).'.\nThe error occurred at the start of your file and no valid FASTQ reads were found.\nThe error in your file occurs between lines '1' and '3', which corresponds to byte-offsets '0' and '33', and contains the text (33 of 33 bytes shown):\n\n@FAKE-1\nACGTACGTAC\n+invalid line\n\n", + "stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/gx-fastq-groomer\", line 10, in \n sys.exit(main())\n ^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 99, in main\n Groomer().run()\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 48, in run\n for read_count, fastq_read in enumerate(reader):\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 683, in __iter__\n yield next(self)\n ^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 742, in __next__\n raise e\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 724, in __next__\n block = super(fastqVerboseErrorReader, self).__next__()\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 621, in __next__\n self._read_fastq_sequence(rval, id_line)\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 666, in _read_fastq_sequence\n raise fastqFormatError(\ngalaxy_utils.sequence.fastq.fastqFormatError: Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).\n", + "job_messages": [], + "dependencies": [], + "job_metrics": [ + { + "title": "Job Runtime (Wall Clock)", + "value": "1 second", + "plugin": "core", + "name": "runtime_seconds", + "raw_value": "1.0000000" + }, + { + "title": "Job End Time", + "value": "2024-09-03 06:30:48", + "plugin": "core", + "name": "end_epoch", + "raw_value": "1725345048.0000000" + }, + { + "title": "Job Start Time", + "value": "2024-09-03 06:30:47", + "plugin": "core", + "name": "start_epoch", + "raw_value": "1725345047.0000000" + }, + { + "title": "Memory Allocated (MB)", + "value": "8160", + "plugin": "core", + "name": "galaxy_memory_mb", + "raw_value": "8160.0000000" + }, + { + "title": "Cores Allocated", + "value": "1", + "plugin": "core", + "name": "galaxy_slots", + "raw_value": "1.0000000" + } + ] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/f92ede2d6e839cb1.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/f92ede2d6e839cb1.json new file mode 100644 index 000000000..d488c1065 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/errors/f92ede2d6e839cb1.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "f92ede2d6e839cb1", + "history_id": "c5fe43971bba42f1", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-03T06:33:28.387845", + "update_time": "2024-09-03T06:33:38.588827", + "galaxy_version": "24.1", + "external_id": "gxy-8gxkk", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/27/registry.xml' '/galaxy/server/database/jobs_directory/000/27/upload_params.json' 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+298614057cf949c6,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +1fea3469de8b10eb,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +74c31b4c3f6ca54b,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +17eba957cb30ed6d,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +1c4990bdd00112d8,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +7e4f207331dfd40e,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +b8489c15a5418aa1,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +8a480d7f0222dcfc,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +2c2b2362273f0801,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +f13374bcc7f5a6be,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +efcadb71aa692393,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +f6ad841bb200e556,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +f5a3f30eee5746e9,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +ddf248f53d379e98,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,error,fastq_groomer/1.1.5,,,,,,,,,,, +04be3fcc63c7ff40,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +14a8f68d665c01a1,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +dd38e7891c4d4385,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +57520598933c3fed,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +849c4506f7ff365b,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +5d83826b224ed5bd,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +e5e36224a481962e,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +985a619d6854de88,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +e68c72fe92db49a4,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +1e0ca3198f45ab6b,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +a988b3758b1cf6df,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +e5e8cd249a50a76f,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +4116c1de5a40792c,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +f92ede2d6e839cb1,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,error,upload1,,,,,,,,,,, +c18be95c05ac52c6,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +10ea677b4495a336,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +c897c618250cf7d5,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,1.0000000 +cf4925c22d908ffb,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +abad5501dcd12988,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +46c327a6d434e72f,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +7031160045e6798a,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +5289d5954fed9550,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +b00016d73b432039,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,error,fastq_groomer/1.1.5,,,,,,,,,,, +e9f7c7443e767705,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +e568629811fc8172,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,error,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,1.0000000 +02710b4481840932,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +cddc15d48be5f26e,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +a4f6ceefe39eba95,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +0598013d15530eee,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,fastq_groomer/1.1.5,,,,8160.0000000,1.0000000,,,,,,0E-7 +06a7ae93479edc6f,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 +fe8ea7347ff1b547,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,deeptools_bigwig_compare/3.3.2.0.0,,,,25769.0000000,8.0000000,,,,,,1.0000000 +61497926af45aba7,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +23615efc68edca36,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,deeptools_bigwig_compare/3.3.2.0.0,,,,25769.0000000,8.0000000,,,,,,1.0000000 +cd155ed83a2ec634,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +22f057fa51fff74b,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,miniasm/0.3+galaxy0,,,,34359.0000000,1.0000000,,,,,,1.0000000 +03b1d146c8da1044,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +dc997c570f96510e,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +b8ae0f015a2e06aa,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,miniasm/0.3+galaxy0,,,,34359.0000000,1.0000000,,,,,,1.0000000 +a80664568881873a,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,5.0000000 +c5fe43971bba42f1,c5fe43971bba42f1,anvil-test-2024-09-03-06-25,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/job.log b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/job.log new file mode 100644 index 000000000..92ba2c2f0 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/job.log @@ -0,0 +1,15885 @@ +Paths for the 'interactivetools_map' option are now relative to 'data_dir', remove the leading 'database/' to suppress this warning: database/interactivetools_map.sqlite +Option master_api_key has been deprecated in favor of bootstrap_admin_api_key +DEBUG:yacman.yacman:Patching yaml loader +DEBUG:yacman.yacman1:Using yacman version 0.9.3 +DEBUG:yacman.yacman_future:Using yacman version 0.9.3 +DEBUG:galaxy.app:python path is: /galaxy/server/scripts, /galaxy/server/lib, /galaxy/server/lib, /usr/local/lib/python312.zip, /usr/local/lib/python3.12, /usr/local/lib/python3.12/lib-dynload, /galaxy/server/.venv/lib/python3.12/site-packages +DEBUG:galaxy.config:Configuration directory is /galaxy/server/config +DEBUG:galaxy.config:Data directory is /galaxy/server/database +DEBUG:galaxy.config:Managed config directory is /galaxy/server/config +WARNING:galaxy.config:Paths for the 'interactivetools_map' option are now relative to 'data_dir', remove the leading 'database/' to suppress this warning: database/interactivetools_map.sqlite +WARNING:galaxy.config:Option master_api_key has been deprecated in favor of bootstrap_admin_api_key +WARNING:galaxy.config:Config option 'containers_resolvers_config_file' is deprecated and will be removed in a future release. Please consult the latest version of the sample configuration file. +INFO:alembic.runtime.migration:Context impl PostgresqlImpl. +INFO:alembic.runtime.migration:Will assume transactional DDL. +INFO:galaxy.model.migrations:Your galaxy database is up-to-date +INFO:alembic.runtime.migration:Context impl PostgresqlImpl. +INFO:alembic.runtime.migration:Will assume transactional DDL. +INFO:galaxy.model.migrations:Your tool shed install database is up-to-date +INFO:galaxy.app:Install database targeting Galaxy's database configuration. +WARNING:galaxy.security.vault:No vault configured. We recommend defining the vault_config_file setting in galaxy.yml +DEBUG:galaxy.web_stack:WeblessApplicationStack initialized +DEBUG:galaxy.web_stack:Will attach to pool(s): job-handlers +galaxy.jobs DEBUG 2024-09-03 06:23:38,740 [pN:job_handler_0,p:8,tN:MainThread] Read job configuration from file: /galaxy/server/config/job_conf.yml +galaxy.jobs INFO 2024-09-03 06:23:38,740 [pN:job_handler_0,p:8,tN:MainThread] Job handler assignment methods set to: db-skip-locked +galaxy.jobs INFO 2024-09-03 06:23:38,740 [pN:job_handler_0,p:8,tN:MainThread] Tag [_default_] handlers: job_handler_0 +galaxy.web_stack.handlers DEBUG 2024-09-03 06:23:38,740 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'tpv_dispatcher' +galaxy.jobs DEBUG 2024-09-03 06:23:38,740 [pN:job_handler_0,p:8,tN:MainThread] Done loading job configuration +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,341 [pN:job_handler_0,p:8,tN:MainThread] Loading datatypes from /galaxy/server/lib/galaxy/config/sample/datatypes_conf.xml.sample +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,342 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.h. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,342 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.c. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,342 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cpp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,342 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.py. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,342 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.go. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,342 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.rs. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,343 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cs. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,343 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hep.root. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,343 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:JP2 from the datatype registry for extension jp2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,343 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry for extension ab1. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,344 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry for extension afg. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,345 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.goldenpath:GoldenPath from the datatype registry for extension agp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,345 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_cog_profile. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,346 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_composite. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,346 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension anvio_classifier. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,346 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioContigsDB from the datatype registry for extension anvio_contigs_db. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,346 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioDB from the datatype registry for extension anvio_db. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,346 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioGenomesDB from the datatype registry for extension anvio_genomes_db. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,346 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioPanDB from the datatype registry for extension anvio_pan_db. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,347 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_pfam_profile. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,347 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioProfileDB from the datatype registry for extension anvio_profile_db. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,347 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioSamplesDB from the datatype registry for extension anvio_samples_db. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,347 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension anvio_state. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,347 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.anvio:AnvioStructureDB from the datatype registry for extension anvio_structure_db. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,347 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension anvio_variability. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,348 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry for extension arff. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,348 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Paf from the datatype registry for extension paf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,348 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa1 from the datatype registry for extension gfa1. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,348 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Gfa2 from the datatype registry for extension gfa2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,348 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension asn1. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,348 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension asn1-binary. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,348 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry for extension axt. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,349 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry for extension fli. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,349 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry for extension bam. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,349 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bai. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,349 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamInputSorted from the datatype registry for extension qname_input_sorted.bam. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,349 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamQuerynameSorted from the datatype registry for extension qname_sorted.bam. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,349 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BamNative from the datatype registry for extension unsorted.bam. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,349 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ProBam from the datatype registry for extension probam. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,349 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry for extension cram. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,350 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry for extension bed. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,350 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry for extension bedgraph. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,350 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry for extension bedstrict. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,350 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry for extension bed6. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,350 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry for extension bed12. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,350 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ProBed from the datatype registry for extension probed. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,350 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry for extension len. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DAA from the datatype registry for extension daa. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RMA6 from the datatype registry for extension rma6. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DMND from the datatype registry for extension dmnd. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Parquet from the datatype registry for extension parquet. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Idat from the datatype registry for extension idat. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry for extension bigbed. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry for extension bigwig. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cxb. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,351 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry for extension chrint. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension csv. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension tsv. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension intermine_tabular. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,352 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry for extension customtrack. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,353 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry for extension bowtie_color_index. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,353 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry for extension bowtie_base_index. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,353 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry for extension csfasta. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,353 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension data. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,353 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,353 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension binary. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension d3_hierarchy. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:ImgtJson from the datatype registry for extension imgt.json. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:GeoJson from the datatype registry for extension geojson. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:DataManagerJson from the datatype registry for extension data_manager_json. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry for extension dbn. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,354 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension fai. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,355 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension fasta. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,355 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastg from the datatype registry for extension fastg. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,355 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry for extension fastq. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,355 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry for extension fastqsanger. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,356 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry for extension fastqsolexa. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,356 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry for extension fastqcssanger. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,356 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry for extension fastqillumina. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry for extension fqtoc. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry for extension eland. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry for extension elandmulti. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry for extension genetrack. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension a3m. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,357 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry for extension gff. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry for extension gff3. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry for extension gif. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry for extension gmaj.zip. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension graph_dot. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,358 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry for extension gtf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension toolshed.gz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hdf4. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension h5. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension scool. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Grib from the datatype registry for extension grib. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Loom from the datatype registry for extension loom. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,359 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Anndata from the datatype registry for extension h5ad. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Visium from the datatype registry for extension visium.tar.gz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mz5. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hyphy_results.json. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hivtrace. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Cool from the datatype registry for extension cool. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MCool from the datatype registry for extension mcool. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:H5MLM from the datatype registry for extension h5mlm. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:LudwigModel from the datatype registry for extension ludwig_model. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,360 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension html. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension ludwig_report.html. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry for extension interval. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension jellyfish. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_ktab. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_hist. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_prof. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,361 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Numpy from the datatype registry for extension npy. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,467 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaTab from the datatype registry for extension isa-tab. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,467 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.isa:IsaJson from the datatype registry for extension isa-json. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,467 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension picard_interval_list. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,467 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_interval. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,468 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_report. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,468 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_dbsnp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,468 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_tranche. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,468 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_recal. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,468 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cnn. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,468 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cns. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,469 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cnr. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,469 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hhr. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,469 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry for extension jpg. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,469 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tiff. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,469 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,469 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf8. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,469 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension btf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,469 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tif. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,470 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension svs. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,470 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension scn. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,470 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension bif. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,470 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:OMETiff from the datatype registry for extension ome.tiff. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,470 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vms. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,470 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vmu. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,470 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension ndpi. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,470 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry for extension mrxs. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,470 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry for extension svslide. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry for extension bmp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry for extension im. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry for extension pcd. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry for extension pcx. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry for extension ppm. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry for extension psd. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry for extension xbm. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry for extension xpm. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry for extension rgb. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry for extension pbm. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry for extension pgm. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nrrd. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,471 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nhdr. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,472 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry for extension rna_eps. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,472 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Artifact from the datatype registry for extension qza. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,473 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Visualization from the datatype registry for extension qzv. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,473 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Metadata from the datatype registry for extension qiime2.tabular. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,473 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension zip. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,473 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension ncbi_genome_dataset.zip. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,473 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension tar. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,473 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension directory. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,473 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension yaml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,473 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mrm. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,476 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Dta from the datatype registry for extension dta. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,476 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Dta2d from the datatype registry for extension dta2d. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,476 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Edta from the datatype registry for extension edta. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,476 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension pepxml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,476 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension raw_pepxml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,476 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension peptideprophet_pepxml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,476 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension interprophet_pepxml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,476 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry for extension protxml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ParamXml from the datatype registry for extension paramxml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Kroenik from the datatype registry for extension kroenik. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepList from the datatype registry for extension peplist. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PSMS from the datatype registry for extension psms. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry for extension pepxml.tsv. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry for extension protxml.tsv. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry for extension mascotdat. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry for extension mzid. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry for extension idxml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry for extension tandem. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,477 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sirius.ms. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry for extension thermo.raw. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BafTar from the datatype registry for extension brukerbaf.d.tar. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:YepTar from the datatype registry for extension agilentbrukeryep.d.tar. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:TdfTar from the datatype registry for extension brukertdf.d.tar. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MassHunterTar from the datatype registry for extension agilentmasshunter.d.tar. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MassLynxTar from the datatype registry for extension watersmasslynx.raw.tar. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:WiffTar from the datatype registry for extension wiff.tar. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Wiff2Tar from the datatype registry for extension wiff2.tar. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MascotXML from the datatype registry for extension mascotxml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzTab from the datatype registry for extension mztab. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzTab2 from the datatype registry for extension mztab2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,478 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry for extension mzml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:NmrML from the datatype registry for extension nmrml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Meryldb from the datatype registry for extension meryldb. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bref3 from the datatype registry for extension bref3. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry for extension mgf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry for extension wiff. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Wiff2 from the datatype registry for extension wiff2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry for extension mzxml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry for extension mzdata. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry for extension ms2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry for extension mzq. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,479 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry for extension sqlite. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,480 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry for extension mz.sqlite. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,480 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OSW from the datatype registry for extension osw. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,480 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:PQP from the datatype registry for extension pqp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,480 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry for extension traml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,480 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:TrafoXML from the datatype registry for extension trafoxml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,480 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry for extension featurexml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,480 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry for extension consensusxml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,480 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry for extension uniprotxml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,480 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XquestXML from the datatype registry for extension xquest.xml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,480 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XquestSpecXML from the datatype registry for extension spec.xml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,480 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:QCML from the datatype registry for extension qcml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,480 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension mzqc. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,481 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry for extension msp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,481 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry for extension splib_noindex. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,481 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry for extension splib. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,481 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BlibSQlite from the datatype registry for extension blib. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,481 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:DlibSQlite from the datatype registry for extension dlib. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,481 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ElibSQlite from the datatype registry for extension elib. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,481 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry for extension hlf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,481 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry for extension idpdb. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,481 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry for extension sf3. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,481 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cps. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,481 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry for extension ct. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:PostgresqlArchive from the datatype registry for extension postgresql. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MongoDBArchive from the datatype registry for extension mongodb. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GeneNoteBook from the datatype registry for extension genenotebook. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry for extension searchgui_archive. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry for extension fast5.tar. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry for extension fast5.tar.gz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry for extension fast5.tar.bz2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveXz from the datatype registry for extension fast5.tar.xz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Pod5 from the datatype registry for extension pod5. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension peptideshaker_archive. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,482 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension percin. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,483 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension percout. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,483 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hardklor. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,483 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension kronik. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,484 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry for extension imzml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,484 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Analyze75 from the datatype registry for extension analyze75. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,484 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nifti1 from the datatype registry for extension nii1. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,484 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Nifti2 from the datatype registry for extension nii2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,485 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Gifti from the datatype registry for extension gii. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,485 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Tck from the datatype registry for extension tck. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,485 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Trk from the datatype registry for extension trk. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,485 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Mrc2014 from the datatype registry for extension mrc. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,485 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Star from the datatype registry for extension star. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,485 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.proteomics:PEFF from the datatype registry for extension peff. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,485 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension toml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,485 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension colab.tar. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,486 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.flow:FCS from the datatype registry for extension fcs. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,486 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowtext. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,486 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowclr. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,486 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowmfi. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,486 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat1. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,486 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,487 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat3. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,487 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowscore. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,487 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowframe. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,487 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension fsom. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,487 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowset. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,487 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension metacyto_clr.txt. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,488 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.metacyto:mSummary from the datatype registry for extension metacyto_summary.txt. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,488 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.metacyto:mStats from the datatype registry for extension metacyto_stats.txt. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,488 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_compute_matrix_archive. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,488 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_coverage_matrix. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,488 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry for extension netcdf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,488 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry for extension eps. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,488 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry for extension rast. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,488 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry for extension laj. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,488 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry for extension lav. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,489 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry for extension maf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,489 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry for extension mafcustomtrack. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,489 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:MatrixMarket from the datatype registry for extension mtx. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,489 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CMAP from the datatype registry for extension cmap. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,489 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry for extension encodepeak. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,489 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension 4dn_pairs. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,489 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension 4dn_pairsam. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,489 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry for extension pdf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,489 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry for extension pileup. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,490 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Psl from the datatype registry for extension psl. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,490 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry for extension obo. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,490 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry for extension owl. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,490 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry for extension png. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,490 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry for extension qual. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,490 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry for extension qualsolexa. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,490 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry for extension qualillumina. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,490 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry for extension qualsolid. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,490 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry for extension qual454. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,490 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry for extension roadmaps. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,491 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry for extension sam. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,491 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry for extension scf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,491 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry for extension sequences. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,491 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry for extension snpeffdb. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,491 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry for extension snpsiftdbnsfp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,491 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dbnsfp.tabular. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,491 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry for extension sff. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,491 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry for extension sra. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,491 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:SraManifest from the datatype registry for extension sra_manifest.tabular. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,491 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension svg. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,492 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry for extension taxonomy. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,492 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension tabular. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,492 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry for extension twobit. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,492 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:SQmass from the datatype registry for extension sqmass. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,492 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry for extension gemini.sqlite. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,492 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ChiraSQLite from the datatype registry for extension chira.sqlite. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,492 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CuffDiffSQlite from the datatype registry for extension cuffdiff.sqlite. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,492 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GAFASQLite from the datatype registry for extension gafa.sqlite. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,492 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:NcbiTaxonomySQlite from the datatype registry for extension ncbitaxonomy.sqlite. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,492 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension txt. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,493 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry for extension linecount. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,493 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry for extension memepsp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,493 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry for extension memexml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,493 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry for extension cisml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,493 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,493 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xsd. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,493 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Dzi from the datatype registry for extension dzi. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,493 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry for extension vcf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,493 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,493 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf_bgzip. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,494 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry for extension bcf_uncompressed. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,494 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry for extension velvet. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,494 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry for extension wig. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,494 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension interval_index. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,494 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension odgi. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,494 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension vg. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,494 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension xg. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,494 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,494 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf3. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,495 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension onnx. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,495 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tabix. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,495 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:IntervalTabix from the datatype registry for extension interval_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,495 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:JuicerMediumTabix from the datatype registry for extension juicer_medium_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,495 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:BedTabix from the datatype registry for extension bed_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,495 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:GffTabix from the datatype registry for extension gff_tabix.gz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,495 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bgzip. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,495 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry for extension vcf_bgzip. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,495 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bus. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,496 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension kallisto.idx. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,496 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry for extension phyloxml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,496 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension newick. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,496 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension nhx. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,496 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry for extension nex. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,496 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:IQTree from the datatype registry for extension iqtree. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,498 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mldist. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,500 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry for extension affybatch. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,500 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry for extension eigenstratgeno. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry for extension eigenstratpca. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry for extension eset. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry for extension fped. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry for extension fphe. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry for extension gg. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry for extension ldindep. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry for extension malist. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry for extension lped. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,501 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry for extension pbed. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry for extension pheno. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry for extension pphe. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry for extension rexpbase. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry for extension rgenetics. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry for extension snptest. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry for extension snpmatrix. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension xls. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry for extension ipynb. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension json. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,502 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:ExpressionJson from the datatype registry for extension expression.json. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,504 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry for extension xgmml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,504 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry for extension sif. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry for extension triples. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry for extension hdt. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry for extension nt. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry for extension n3. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry for extension ttl. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry for extension rdf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry for extension jsonld. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.triples:Sbol from the datatype registry for extension sbol. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension excel.xls. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry for extension xlsx. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,506 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension docx. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,507 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension btwisted. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,507 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cai. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,507 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cat_db. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,507 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension charge. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,507 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension checktrans. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,507 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension chips. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,507 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codcmp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension coderet. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension compseq. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgplot. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgreport. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cusp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cut. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dan. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension digest. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,508 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dreg. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,509 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension einverted. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,509 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension epestfind. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,509 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension equicktandem. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,509 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension est2genome. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,509 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension etandem. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,509 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension freak. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,509 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzznuc. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,509 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzzpro. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzztran. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension garnier. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension geecee. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension helixturnhelix. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hmoment. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension isochore. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension match. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nametable. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension needle. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,510 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgreport. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,511 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgseek. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,511 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension noreturn. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,511 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension palindrome. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,511 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepcoil. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,511 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepinfo. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,511 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepstats. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,511 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension polydot. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,511 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension preg. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,511 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prettyseq. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,512 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension primersearch. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,512 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showfeat. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,512 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showorf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,512 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sixpack. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,512 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension strider. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,512 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension supermatcher. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,512 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension syco. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,512 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension textsearch. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,512 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension vectorstrip. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,512 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wobble. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,513 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wordcount. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,513 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dbmotif. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,513 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension diffseq. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,513 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension excel. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,513 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feattable. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,513 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension motif. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,513 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension regions. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,513 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension seqtable. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,513 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension simple. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,514 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension table. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,514 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension tagseq. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,514 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension acedb. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,514 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension clustal. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,514 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codata. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,514 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension embl. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,514 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fitch. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,514 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gcg. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,514 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry for extension genbank. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,515 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hennig86. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,515 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ig. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,515 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifer. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,515 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifernon. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,515 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mega. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,515 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension meganon. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,515 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ncbi. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,515 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexus. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,516 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexusnon. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,516 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.phylip:Phylip from the datatype registry for extension phylip. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,516 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension phylipnon. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,516 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pir. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,516 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension staden. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,517 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension swiss. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,518 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Msf from the datatype registry for extension msf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,518 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx0. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,518 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx1. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,518 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx10. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,518 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,518 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx3. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,518 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pair. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,519 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension score. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,519 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srs. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,519 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srspair. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,520 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry for extension snaphmm. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,520 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry for extension augustus. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,520 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:ICM from the datatype registry for extension icm. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,520 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:InfernalCM from the datatype registry for extension cm. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,520 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry for extension hmm2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,520 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry for extension hmm3. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,520 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry for extension stockholm. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,521 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry for extension xmfa. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,521 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Cel from the datatype registry for extension cel. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,521 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gpr from the datatype registry for extension gpr. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,521 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.microarrays:Gal from the datatype registry for extension gal. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,522 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension rds. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,522 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension phyloseq. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,522 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,522 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.sce. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,522 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.raw. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,522 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.msnbase.raw. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,522 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.findchrompeaks. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,522 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.group. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,523 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.retcor. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,523 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.fillpeaks. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,523 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.positive. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,523 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.negative. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,523 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.quick. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,524 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.hdf5:HDF5SummarizedExperiment from the datatype registry for extension rdata.se. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,524 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rdock_as. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,524 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry for extension oxlicg. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,524 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry for extension oxling. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,524 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry for extension oxlits. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,524 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry for extension oxlist. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,524 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry for extension oxliss. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,524 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry for extension oxligl. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,526 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry for extension stl. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,526 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry for extension plyascii. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,526 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry for extension plybinary. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,526 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry for extension vtkascii. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,526 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry for extension vtkbinary. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,526 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry for extension biom1. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,526 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry for extension biom2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,526 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:MashSketch from the datatype registry for extension msh. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,527 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry for extension scidx. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,529 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry for extension smi. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,529 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry for extension sdf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,529 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry for extension inchi. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,529 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry for extension mol. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,529 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry for extension mol2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,529 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry for extension cml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,529 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry for extension fps. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,529 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry for extension obfs. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,530 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry for extension drf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,530 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry for extension phar. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,530 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry for extension pdb. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,530 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry for extension pdbqt. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,530 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:PQR from the datatype registry for extension pqr. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,530 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:Cell from the datatype registry for extension cell. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,530 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:CIF from the datatype registry for extension cif. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,530 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:XYZ from the datatype registry for extension xyz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,530 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:ExtendedXYZ from the datatype registry for extension extxyz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,530 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:Magres from the datatype registry for extension magres. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,531 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Trr from the datatype registry for extension trr. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,531 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Dcd from the datatype registry for extension dcd. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,531 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension top. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,531 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prmtop. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,531 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension itp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,531 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mdp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,531 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ndx. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,531 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension xvg. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,532 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Xtc from the datatype registry for extension xtc. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,532 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Cpt from the datatype registry for extension cpt. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,532 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Edr from the datatype registry for extension edr. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,532 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tpr. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,532 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:GRO from the datatype registry for extension gro. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,532 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension inpcrd. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,532 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Vel from the datatype registry for extension vel. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,532 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry for extension grd. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,532 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry for extension grd.tgz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,533 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.otu. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,533 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.list. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,533 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.sabund. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,533 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.rabund. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,533 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.shared. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,533 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.relabund. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,533 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry for extension mothur.names. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,533 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.design. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,534 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry for extension mothur.summary. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,534 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.groups. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,534 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry for extension mothur.oligos. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,534 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension mothur.align. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,534 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.accnos. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,534 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.otulabels. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,534 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mothur.otu.corr. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,534 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry for extension mothur.map. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,535 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry for extension mothur.align.check. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,535 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry for extension mothur.align.report. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,535 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry for extension mothur.filter. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,535 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry for extension mothur.dist. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,535 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mothur.tre. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,535 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry for extension mothur.pair.dist. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,535 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mothur.square.dist. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,535 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry for extension mothur.lower.dist. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,535 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.ref.taxonomy. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,536 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.seq.taxonomy. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,536 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.rdp.taxonomy. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,536 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry for extension mothur.cons.taxonomy. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,536 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry for extension mothur.tax.summary. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,536 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry for extension mothur.freq. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,536 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.quan. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,536 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.quan. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,536 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.masked.quan. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,537 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.masked.quan. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,537 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry for extension mothur.axes. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,537 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry for extension mothur.sff.flow. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,537 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry for extension mothur.count_table. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,538 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry for extension neostore. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,538 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDBzip from the datatype registry for extension neostore.zip. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,538 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry for extension trackhub. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,539 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry for extension blastxml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,539 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry for extension blastdbn. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,539 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry for extension blastdbp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,539 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry for extension blastdbd. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,539 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:LastDb from the datatype registry for extension lastdb. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,539 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb5 from the datatype registry for extension blastdbn5. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,539 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb5 from the datatype registry for extension blastdbp5. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,540 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb5 from the datatype registry for extension blastdbd5. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,540 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension maskinfo-asn1. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,540 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension maskinfo-asn1-binary. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,540 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension pssm-asn1. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,541 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry for extension ptkscmp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,541 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry for extension smat. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,541 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:GenotypeMatrix from the datatype registry for extension alohomora_gts. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,541 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_map. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,541 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_maf. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,541 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_ped. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,541 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension linkage_pedin. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,542 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:DataIn from the datatype registry for extension linkage_datain. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,542 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:MarkerMap from the datatype registry for extension linkage_map. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,542 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_ihaplo. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,542 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_descent. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,542 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:AllegroLOD from the datatype registry for extension allegro_fparam. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,542 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.genetics:IdeasPre from the datatype registry for extension ideaspre. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,542 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.xml:Sbml from the datatype registry for extension sbml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,543 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnNuclDb from the datatype registry for extension spalndbnp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,543 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.spaln:SpalnProtDb from the datatype registry for extension spalndba. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,543 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_dada. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,543 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_errorrates. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,543 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_mergepairs. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,543 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_sequencetable. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,544 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_uniques. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,544 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension ampvis2. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,544 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension ckpt. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,544 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tgz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,552 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Wav from the datatype registry for extension wav. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,552 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mp3 from the datatype registry for extension mp3. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,552 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Ogg from the datatype registry for extension ogg. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,552 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Wma from the datatype registry for extension wma. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,552 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mkv from the datatype registry for extension mkv. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,552 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mp4 from the datatype registry for extension mp4. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,552 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Flv from the datatype registry for extension flv. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,552 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Webm from the datatype registry for extension webm. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,553 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mpg from the datatype registry for extension mpg. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,553 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Mov from the datatype registry for extension mov. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,553 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Avi from the datatype registry for extension avi. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,553 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.media:Wmv from the datatype registry for extension wmv. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,553 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.speech:TextGrid from the datatype registry for extension textgrid. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,553 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.speech:BPF from the datatype registry for extension par. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,553 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension ffindex. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,554 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension ffdata. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,554 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Pretext from the datatype registry for extension pretext. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,554 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension immuneml_receptors.html. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,554 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdMaterials from the datatype registry for extension hexrd.materials.h5. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,554 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension npz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,554 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdImagesNpz from the datatype registry for extension hexrd.images.npz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,554 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:HexrdEtaOmeNpz from the datatype registry for extension hexrd.eta_ome.npz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,554 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension hexrd.scored_orientations.npz. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,554 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hexrd.accepted_orientations. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,555 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension hexrd.yml. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,555 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTess from the datatype registry for extension neper.tess. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,555 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTesr from the datatype registry for extension neper.tesr. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,555 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPoints from the datatype registry for extension neper.points. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,555 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPointsTabular from the datatype registry for extension neper.points.tsv. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,555 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperMultiScaleCell from the datatype registry for extension neper.mscell. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,555 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshMsh from the datatype registry for extension gmsh.msh. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,555 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshGeo from the datatype registry for extension gmsh.geo. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,555 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:ZsetGeof from the datatype registry for extension zset.geof. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,555 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension stl. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,556 [pN:job_handler_0,p:8,tN:MainThread] Overriding conflicting datatype with extension 'stl', using datatype from /galaxy/server/lib/galaxy/config/sample/datatypes_conf.xml.sample. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,556 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Text from the datatype registry for extension pov. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,556 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaResult from the datatype registry for extension pithya.result. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,556 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaProperty from the datatype registry for extension pithya.property. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,556 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:PithyaModel from the datatype registry for extension pithya.model. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,556 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:BCSLts from the datatype registry for extension bcsl.ts. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,556 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:BCSLmodel from the datatype registry for extension bcsl.model. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,556 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:StormSample from the datatype registry for extension storm.sample. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,556 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:StormCheck from the datatype registry for extension storm.check. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,557 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:CTLresult from the datatype registry for extension ctl.result. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,557 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Castep from the datatype registry for extension castep. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,557 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:Param from the datatype registry for extension param. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,557 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.text:FormattedDensity from the datatype registry for extension den_fmt. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,557 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.larch:AthenaProject from the datatype registry for extension prj. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,557 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.larch:FEFFInput from the datatype registry for extension inp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,557 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension sp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,558 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension gds. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,558 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension feff. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,558 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feffit. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,558 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bil. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,558 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hdr. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,559 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.gis:Shapefile from the datatype registry for extension shp. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,559 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.binary:FITS from the datatype registry for extension fits. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,559 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.chain:Chain from the datatype registry for extension chain. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,559 [pN:job_handler_0,p:8,tN:MainThread] Retrieved datatype module galaxy.datatypes.chain:Net from the datatype registry for extension ucsc.net. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,559 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTess' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTesr' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,560 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:GmshMsh' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.goldenpath:GoldenPath' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:JP2' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQmass' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OSW' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PQP' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ElibSQlite' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DlibSQlite' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BlibSQlite' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ChiraSQLite' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CuffDiffSQlite' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:GAFASQLite' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NcbiTaxonomySQlite' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5MLM' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cool' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MCool' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,561 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Loom' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Anndata' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdMaterials' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Grib' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdImagesNpz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdEtaOmeNpz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Npz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamQuerynameSorted' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamNative' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DAA' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RMA6' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Parquet' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:BafTar' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:TdfTar' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassHunterTar' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,562 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassLynxTar' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:YepTar' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:WiffTar' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveXz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pod5' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Meryldb' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bref3' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:PostgresqlArchive' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:ICM' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Idat' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Trr' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Dcd' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xtc' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cpt' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Edr' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Vel' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xlsx' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Numpy' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,563 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Metadata' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Artifact' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Visualization' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedZipArchive' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pretext' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.chain:Chain' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.chain:Net' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gifti' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Dzi' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:Sbml' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Dta2d' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Edta' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ConsensusXML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:IdXML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:FeatureXML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,564 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MascotXML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Ms2' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab2' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ParamXml' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:NmrML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Kroenik' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepList' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PSMS' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,565 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TrafoXML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestXML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestSpecXML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:QCML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Wiff' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PEFF' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Sbol' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,566 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastg' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Cell' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CIF' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:ExtendedXYZ' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:XYZ' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Magres' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,567 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PQR' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.molecules:GRO' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.phylip:Phylip' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqCSSanger' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Html' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,568 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Psl' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Paf' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:IQTree' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,569 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:ImgtJson' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:GeoJson' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaResult' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLts' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Json' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:GenotypeMatrix' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:DataIn' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:MarkerMap' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.genetics:AllegroLOD' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CMAP' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,570 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mSummary' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mStats' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.tabular:MatrixMarket' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.msa:InfernalCM' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Cel' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gpr' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gal' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:RDS' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Mrc2014' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,571 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Png' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:OMETiff' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Im' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,572 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Tck' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Trk' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti1' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti2' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.images:Star' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Wav' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp3' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp4' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Flv' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,573 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Ogg' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mpg' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mov' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Avi' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Wmv' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Wma' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Webm' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.media:Mkv' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:TextGrid' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.speech:BPF' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.larch:FEFFInput' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.larch:AthenaProject' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Castep' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:CTLresult' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,574 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:FormattedDensity' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Param' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:Yaml' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.binary:FITS' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.neo4j:Neo4jDBzip' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaProperty' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,575 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaModel' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,576 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLmodel' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,576 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormSample' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,576 [pN:job_handler_0,p:8,tN:MainThread] Loaded sniffer for datatype 'galaxy.datatypes.text:StormCheck' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,580 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'ucsc': /cvmfs/data.galaxyproject.org/managed/location/ucsc_build_sites.txt with display sites: ['main', 'archaea', 'ucla'] +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,580 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'gbrowse': /galaxy/server/tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['wormbase', 'tair', 'modencode_worm', 'modencode_fly'] +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,580 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'ensembl': /galaxy/server/tool-data/shared/ensembl/ensembl_sites.txt +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,580 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'ensembl_data_url': /galaxy/server/tool-data/shared/ensembl/ensembl_sites_data_URL.txt +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,580 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'igv': /galaxy/server/tool-data/shared/igv/igv_build_sites.txt.sample +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:39,580 [pN:job_handler_0,p:8,tN:MainThread] Loaded build site 'rviewer': /galaxy/server/tool-data/shared/rviewer/rviewer_build_sites.txt.sample +galaxy.util.tool_shed.tool_shed_registry DEBUG 2024-09-03 06:23:39,581 [pN:job_handler_0,p:8,tN:MainThread] Loading references to tool sheds from internal default config +galaxy.util.tool_shed.tool_shed_registry DEBUG 2024-09-03 06:23:39,582 [pN:job_handler_0,p:8,tN:MainThread] Loaded reference to tool shed: Galaxy Main Tool Shed +galaxy.web_stack DEBUG 2024-09-03 06:23:39,583 [pN:job_handler_0,p:8,tN:MainThread] server_name set to: job_handler_0 +galaxy.queue_worker INFO 2024-09-03 06:23:39,588 [pN:job_handler_0,p:8,tN:MainThread] Initializing job_handler_0 Galaxy Queue Worker on amqp://default_user_6GOCjkQNG8bLAza2TkU:********@edge-24-09-03-06-11-1-galaxy-rabbitmq-server:5672 +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,599 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/db536ad45f28/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,599 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,599 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ee2beb764a7b/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,599 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,599 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/78bbd17d0703/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,599 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,599 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/7fe36019c073/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,599 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,599 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/2cf4a1cafc16/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,600 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,600 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/f95f403841ad/primer_scheme_bedfiles.loc' for tool data table 'primer_scheme_bedfiles' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,600 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'primer_scheme_bedfiles' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,600 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/d6dc477167f8/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,600 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,600 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/672b6c02fbc7/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,600 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,600 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/365325116147/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,600 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,600 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/fec517907949/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,600 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,600 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/c077f71d351f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,601 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,601 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/ed4ea9de1791/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,601 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,601 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/dfef7a353ed0/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,601 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,601 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/01d6b7d6365e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,601 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,601 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/8abfcd1a6949/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,601 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,601 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/4813f99d81b7/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,601 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,602 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/0dbff46d5a1b/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,602 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,602 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bf235558f2cf/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,602 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,602 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/d40d4bf05718/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,602 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,602 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/b8e9da766b0f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,602 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,602 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/776ad0b21536/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,602 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,602 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/9ef52d95114b/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,602 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,603 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/b17394940c7a/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,603 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,603 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/582f8b13873d/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,603 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,603 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bf7d6acd9884/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,603 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,603 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/02f349bdbf96/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,603 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,603 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/e03f2f3ac3a9/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,603 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,604 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/b76adb2f1c51/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,604 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,604 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/072f606e2e69/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,604 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,604 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/23680a42e149/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,604 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,604 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/6ca7c55a27e8/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,604 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,604 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/fdd127bd4a32/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,604 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,604 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/403553ae19f6/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,604 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,605 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/5c232a738c74/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,605 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,605 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/c9c5718edc19/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,605 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,605 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bdfdf5f6e950/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,605 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,605 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/2968c6916579/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,605 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,605 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/a3dea556218d/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,605 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,605 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/29f9b782727e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,605 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,606 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/17096387c0e6/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,606 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,606 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/166c4f50525f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,606 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,606 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,606 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,606 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,606 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,606 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/all_gff.loc' for tool data table 'all_gff' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,606 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'all_gff' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,606 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/ce3c7f062223/dbkeys.loc' for tool data table '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,607 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table '__dbkeys__' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,607 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/093678460093/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,607 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,607 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/7d37cfda8e00/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,607 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,607 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "all_fasta", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,607 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/circos/df7356989ac1/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,607 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,607 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/4542035c1075/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,607 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,607 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/minimap2/f54f5baedfdd/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,607 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,608 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/09b2cdb7ace5/bowtie2_indices.loc' for tool data table 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,608 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bowtie2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,608 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/3fe632431b68/bwa_mem_index.loc' for tool data table 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,608 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwa_mem_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,608 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bwameth/29bdbc353f20/bwameth_indexes.loc' for tool data table 'bwameth_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,608 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwameth_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,608 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/lastz/e7f19d6a9af8/lastz_seqs.loc' for tool data table 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,608 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'lastz_seqs' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,608 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/43815fa60f3a/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,609 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,609 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/a7228a7ea146/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,609 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,609 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/336b3def9b2b/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,609 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,609 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/db25ec99c3ea/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,609 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,609 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/salmon/cc05793bb896/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,609 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,609 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/a8f343909c17/sailfish_indexes.loc' for tool data table 'sailfish_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,609 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'sailfish_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,609 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/26371a1df031/hisat2_indexes.loc' for tool data table 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,609 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'hisat2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,610 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/stringtie/1ebd14235b92/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,610 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,610 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/b72793637686/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,610 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,610 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/a3b4ad6858ff/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,610 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,610 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bamtools/4d343c1f606b/sam_fa_indices.loc' for tool data table 'sam_fa_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,610 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'sam_fa_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,610 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/145f6d74ff5e/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,610 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,611 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/06dc50b7b711/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,611 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,611 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/fa7ad9b89f4a/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,611 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,611 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/cf1ffd88f895/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,611 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,611 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/e1461b5c52a0/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,611 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,611 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/aa35ee7f3ab2/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,611 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,611 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/426d707dfc47/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,611 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,611 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/7dfca164d2e3/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,612 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,612 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/09d6e4693887/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,612 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,612 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/ef2c525bd8cd/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,612 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,612 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/d12a810c837e/snpeff_msigdb_database.loc' for tool data table 'snpeff_msigdb_database' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpeff_msigdb_database' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,612 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/4e21e4f2bc48/snpsift_dbnsfps.loc' for tool data table 'snpsift_dbnsfps' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpsift_dbnsfps' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,612 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/74aebe30fb52/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,612 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,613 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/74aebe30fb52/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,613 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,613 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/2b62154e39c8/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,613 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,613 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,613 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,613 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/alevin/e4c01dcece8b/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,613 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,613 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/88c07fc4024c/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,613 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,613 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/093678460093/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,613 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,614 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/7d37cfda8e00/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,614 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,614 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/c772497b2c32/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,614 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/eec9494fdafa/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,614 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,614 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/38b6d12edc68/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,614 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,614 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/38b6d12edc68/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,614 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,614 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/alevin/ecb9ea6269ee/salmon_indexes_versioned.loc' for tool data table 'salmon_indexes_versioned' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,615 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'salmon_indexes_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,615 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/2055c2667eb3/rnastar_index2.loc' for tool data table 'rnastar_index2' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,615 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'rnastar_index2' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,615 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/f3a5f075498f/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,615 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,615 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/f3a5f075498f/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,615 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,615 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/24c5d43cb545/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,615 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,615 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/07e8b80f278c/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,615 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,616 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/07e8b80f278c/all_gff.loc' for tool data table 'all_gff' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,616 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_gff' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,616 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/07e8b80f278c/dbkeys.loc' for tool data table '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,616 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,616 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/135b80fb1ac2/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,616 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,616 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/980d2a2e1180/rnastar_index2x_versioned.loc' for tool data table 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,616 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,616 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/b502c227b5e6/picard_index.loc' for tool data table 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,616 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'picard_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,616 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/f4af63aaf57a/hisat2_indexes.loc' for tool data table 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,616 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,616 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c5e2e5902201/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,616 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,617 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/660cffd8d92a/adapters.loc' for tool data table 'adapters' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,617 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'adapters' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,617 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/e3ba567abdf5/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,617 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,617 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/e3ba567abdf5/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,617 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,617 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/f088370d2a3c/all_fasta.loc' for tool data table 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,617 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,617 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/f088370d2a3c/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,617 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,618 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/e188dc7a68e6/bwa_mem_index.loc' for tool data table 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,618 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,618 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/a1f0b3f4b781/picard_index.loc' for tool data table 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,618 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,618 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/picard/b9fbec5ac6b2/picard_index.loc' for tool data table 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,618 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,618 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/hisat2/61ee47027bd3/hisat2_indexes.loc' for tool data table 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,618 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,618 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/1759d845181e/gene_sets.loc' for tool data table 'gene_sets' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,618 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gene_sets' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,618 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/1759d845181e/featurecounts_anno.loc' for tool data table 'featurecounts_anno' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,618 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'featurecounts_anno' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,619 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/d080005cffe1/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,619 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,619 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/5826298f6a73/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,619 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,619 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/0dbf49c414ae/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,619 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,619 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/4805fe3d8fda/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,619 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,619 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/65432c3abf6c/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,619 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,619 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/2270a8b83c12/gemini_versioned_databases.loc' for tool data table 'gemini_versioned_databases' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,619 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gemini_versioned_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,620 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/cf61daf064fe/gemini_databases.loc' for tool data table 'gemini_databases' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,620 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gemini_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,620 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/c2a413e47fe9/gemini_versioned_databases.loc' for tool data table 'gemini_versioned_databases' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,620 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_versioned_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,620 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/4c5f4e9b1931/gemini_databases.loc' for tool data table 'gemini_databases' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,620 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,620 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/77a1e60fd1de/gemini_versioned_databases.loc' for tool data table 'gemini_versioned_databases' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,620 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_versioned_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,620 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/666f60a9331a/gemini_databases.loc' for tool data table 'gemini_databases' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,620 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'gemini_databases' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,620 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/a5937157062f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,620 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,620 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/freebayes/156b60c1530f/fasta_indexes.loc' for tool data table 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,621 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,621 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/5b80f544c67f/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,621 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,621 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/5b80f544c67f/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,621 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,621 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/68693743661e/snpeffv_genomedb.loc' for tool data table 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,621 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,621 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/tmp/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/68693743661e/snpeffv_regulationdb.loc' for tool data table 'snpeffv_regulationdb' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,621 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_regulationdb' from file '/cvmfs/cloud.galaxyproject.org/config/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,624 [pN:job_handler_0,p:8,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/managed/location/all_fasta_dbkeys.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,624 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,625 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/managed/location/dbkeys.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,625 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,626 [pN:job_handler_0,p:8,tN:MainThread] Loaded 18 lines from '/cvmfs/data.galaxyproject.org/managed/location/all_fasta.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,626 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,627 [pN:job_handler_0,p:8,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/alignseq.loc' for 'alignseq_seq' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,628 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'alignseq_seq' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/twobit.loc' for 'twobit' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,629 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'twobit' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,630 [pN:job_handler_0,p:8,tN:MainThread] Loaded 21 lines from '/cvmfs/data.galaxyproject.org/managed/location/lastz_seqs.loc' for 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,630 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,631 [pN:job_handler_0,p:8,tN:MainThread] Loaded 35 lines from '/cvmfs/data.galaxyproject.org/managed/location/bowtie2_indices.loc' for 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,632 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bowtie2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded 35 lines from '/cvmfs/data.galaxyproject.org/managed/location/tophat2_indices.loc' for 'tophat2_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,633 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'tophat2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,634 [pN:job_handler_0,p:8,tN:MainThread] Loaded 59 lines from '/cvmfs/data.galaxyproject.org/managed/location/hisat2_indexes.loc' for 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,634 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,634 [pN:job_handler_0,p:8,tN:MainThread] Attempted to add fields (['ce9', 'ce9', 'C. elegans (WS210): ce9', '/cvmfs/data.galaxyproject.org/managed/hisat2_index/ce9/ce9']) to data table 'hisat2_indexes', but this entry already exists and allow_duplicates is False. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,636 [pN:job_handler_0,p:8,tN:MainThread] Loaded 47 lines from '/cvmfs/data.galaxyproject.org/managed/location/bwa_mem_index.loc' for 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,636 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,636 [pN:job_handler_0,p:8,tN:MainThread] Attempted to add fields (['papHam1', 'papHam1', 'Baboon (Papio anubis): papHam1', '/cvmfs/data.galaxyproject.org/managed/bwa_mem_index/papHam1/papHam1.fa']) to data table 'bwa_mem_indexes', but this entry already exists and allow_duplicates is False. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,637 [pN:job_handler_0,p:8,tN:MainThread] Loaded 20 lines from '/cvmfs/data.galaxyproject.org/managed/location/fasta_indexes.loc' for 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,637 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,638 [pN:job_handler_0,p:8,tN:MainThread] Loaded 19 lines from '/cvmfs/data.galaxyproject.org/managed/location/picard_index.loc' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,638 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/managed/location/kraken_databases.loc' for 'kraken_databases' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,641 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'kraken_databases' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/managed/location/ncbi_taxonomy.loc' for 'ncbi_taxonomy' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,642 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_taxonomy' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,646 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1193 lines from '/cvmfs/data.galaxyproject.org/managed/location/dbkeys_ucsc.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,646 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,679 [pN:job_handler_0,p:8,tN:MainThread] Loaded 14 lines from '/cvmfs/data.galaxyproject.org/managed/location/rnastar_index2.loc' for 'rnastar_index2' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,679 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/managed/location/plant_tribes_scaffolds.loc' for 'plant_tribes_scaffolds' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,681 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'plant_tribes_scaffolds' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/managed/location/maf_indexes.loc' for 'maf_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,682 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'maf_indexes' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,683 [pN:job_handler_0,p:8,tN:MainThread] Loaded 15 lines from '/cvmfs/data.galaxyproject.org/managed/location/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,683 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded 19 lines from '/cvmfs/data.galaxyproject.org/managed/location/kraken2_databases.loc' for 'kraken2_databases' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,684 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'kraken2_databases' from file '/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,688 [pN:job_handler_0,p:8,tN:MainThread] Loaded 237 lines from '/cvmfs/data.galaxyproject.org/byhand/location/all_fasta.loc' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,688 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,689 [pN:job_handler_0,p:8,tN:MainThread] Attempted to add fields (['ornAna1', 'ornAna1', 'Platypus (Ornithorhynchus anatinus): ornAna1', '/cvmfs/data.galaxyproject.org/byhand/ornAna1/seq/ornAna1.fa']) to data table 'all_fasta', but this entry already exists and allow_duplicates is False. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,691 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dbkeys.loc' for '__dbkeys__' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,691 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,692 [pN:job_handler_0,p:8,tN:MainThread] Loaded 5 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bfast_indexes.loc' for 'bfast_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,692 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bfast_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded 6 lines from '/cvmfs/data.galaxyproject.org/byhand/location/blastdb.loc' for 'blastdb' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,693 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'blastdb' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,694 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/blastdb_p.loc' for 'blastdb_p' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,695 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'blastdb_p' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,696 [pN:job_handler_0,p:8,tN:MainThread] Loaded 122 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie2_indices.loc' for 'bowtie2_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,696 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bowtie2_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,698 [pN:job_handler_0,p:8,tN:MainThread] Loaded 16 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_mem_index.loc' for 'bwa_mem_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,698 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded 201 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_index.loc' for 'bwa_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,700 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwa_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded 9 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwa_index_color.loc' for 'bwa_indexes_color' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,701 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bwa_indexes_color' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,703 [pN:job_handler_0,p:8,tN:MainThread] Loaded 24 lines from '/cvmfs/data.galaxyproject.org/byhand/location/maf_index.loc' for 'indexed_maf_files' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,703 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'indexed_maf_files' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,704 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ngs_sim_fasta.loc' for 'ngs_sim_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,704 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ngs_sim_fasta' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,705 [pN:job_handler_0,p:8,tN:MainThread] Loaded 10 lines from '/cvmfs/data.galaxyproject.org/byhand/location/perm_base_index.loc' for 'perm_base_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,705 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'perm_base_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded 10 lines from '/cvmfs/data.galaxyproject.org/byhand/location/perm_color_index.loc' for 'perm_color_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,706 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'perm_color_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,707 [pN:job_handler_0,p:8,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/picard_index.loc' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,707 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/gatk_sorted_picard_index.loc' for 'gatk_picard_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gatk_picard_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,709 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file '/cvmfs/data.galaxyproject.org/byhand/location/gatk_annotations.txt' for tool data table 'gatk_annotations' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,709 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'gatk_annotations' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/picard_index.loc' for 'srma_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,711 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'srma_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,714 [pN:job_handler_0,p:8,tN:MainThread] Loaded 202 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices.loc' for 'tophat_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,714 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'tophat_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,715 [pN:job_handler_0,p:8,tN:MainThread] Loaded 194 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices_color.loc' for 'tophat_indexes_color' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,715 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'tophat_indexes_color' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,717 [pN:job_handler_0,p:8,tN:MainThread] Loaded 122 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie2_indices.loc' for 'tophat2_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,717 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'tophat2_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,718 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ccat_configurations.loc' for 'ccat_configurations' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,718 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ccat_configurations' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,720 [pN:job_handler_0,p:8,tN:MainThread] Loaded 182 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mosaik_index.loc' for 'mosaik_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,720 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'mosaik_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,722 [pN:job_handler_0,p:8,tN:MainThread] Loaded 202 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices.loc' for 'bowtie_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,722 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bowtie_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,723 [pN:job_handler_0,p:8,tN:MainThread] Loaded 194 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bowtie_indices_color.loc' for 'bowtie_indexes_color' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,723 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bowtie_indexes_color' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,725 [pN:job_handler_0,p:8,tN:MainThread] Loaded 192 lines from '/cvmfs/data.galaxyproject.org/byhand/location/lastz_seqs.loc' for 'lastz_seqs' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,725 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'lastz_seqs' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,728 [pN:job_handler_0,p:8,tN:MainThread] Loaded 180 lines from '/cvmfs/data.galaxyproject.org/byhand/location/sam_fa_indices.loc' for 'sam_fa_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,728 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'sam_fa_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,731 [pN:job_handler_0,p:8,tN:MainThread] Loaded 177 lines from '/cvmfs/data.galaxyproject.org/byhand/location/fasta_indexes.loc' for 'fasta_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,731 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,736 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1181 lines from '/cvmfs/data.galaxyproject.org/byhand/location/liftOver.loc' for 'liftOver' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,736 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'liftOver' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,737 [pN:job_handler_0,p:8,tN:MainThread] Loaded 25 lines from '/cvmfs/data.galaxyproject.org/byhand/location/twobit.loc' for 'twobit' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,737 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'twobit' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,738 [pN:job_handler_0,p:8,tN:MainThread] Loaded 106 lines from '/cvmfs/data.galaxyproject.org/byhand/location/customProDB.loc' for 'customProDB' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,738 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'customProDB' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,739 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/hisat2_indexes.loc' for 'hisat2_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,739 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,740 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/rnastar_index2x_versioned.loc' for 'rnastar_index2x_versioned' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,740 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'rnastar_index2x_versioned' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,741 [pN:job_handler_0,p:8,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/byhand/location/snpeffv_genomedb.loc' for 'snpeffv_genomedb' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,741 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'snpeffv_genomedb' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,742 [pN:job_handler_0,p:8,tN:MainThread] Loaded 5 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bwameth_indexes.loc' for 'bwameth_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,742 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwameth_indexes' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,743 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/metaphlan_database_versioned.loc' for 'metaphlan_database_versioned' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,743 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'metaphlan_database_versioned' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,744 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/busco_database.loc' for 'busco_database' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,744 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'busco_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,745 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_fcs_gx_config.tsv' for 'ncbi_fcs_gx_config' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,745 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_fcs_gx_config' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,746 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_fcs_gx_databases.loc' for 'ncbi_fcs_gx_databases' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,746 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_fcs_gx_databases' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,747 [pN:job_handler_0,p:8,tN:MainThread] Loaded 63 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_fcs_gx_divisions.tsv' for 'ncbi_fcs_gx_divisions' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,747 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'ncbi_fcs_gx_divisions' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,748 [pN:job_handler_0,p:8,tN:MainThread] Loaded 8 lines from '/cvmfs/data.galaxyproject.org/byhand/location/rRNA_databases.loc' for 'rRNA_databases' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,748 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'rRNA_databases' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,749 [pN:job_handler_0,p:8,tN:MainThread] Loaded 6 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mitos.loc' for 'mitos' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,749 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'mitos' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,750 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dada2_species.loc' for 'dada2_species' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,750 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'dada2_species' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,751 [pN:job_handler_0,p:8,tN:MainThread] Loaded 9 lines from '/cvmfs/data.galaxyproject.org/byhand/location/dada2_taxonomy.loc' for 'dada2_taxonomy' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,751 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'dada2_taxonomy' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,752 [pN:job_handler_0,p:8,tN:MainThread] Loaded 4 lines from '/cvmfs/data.galaxyproject.org/byhand/location/mapseq_db.loc' for 'mapseq_db' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,752 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'mapseq_db' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,752 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bracken_databases.loc' for 'bracken_databases' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,752 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bracken_databases' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,753 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/plasmidfinder_database.loc' for 'plasmidfinder_database' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,753 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'plasmidfinder_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,754 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/amrfinderplus.loc' for 'amrfinderplus_database' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,754 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'amrfinderplus_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/cvmfs/data.galaxyproject.org/byhand/location/amrfinderplus_versioned.loc' for 'amrfinderplus_versioned_database' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'amrfinderplus_versioned_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded 2 lines from '/cvmfs/data.galaxyproject.org/byhand/location/bakta_database.loc' for 'bakta_database' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bakta_database' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,888 [pN:job_handler_0,p:8,tN:MainThread] Loaded 3 lines from '/cvmfs/data.galaxyproject.org/byhand/location/ncbi_taxonomy.loc' for 'ncbi_taxonomy' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,888 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'ncbi_taxonomy' from file '/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data INFO 2024-09-03 06:23:39,890 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/all_fasta.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,892 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/all_fasta.loc.sample' for 'all_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,893 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data INFO 2024-09-03 06:23:39,893 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/bfast_indexes.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,894 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,894 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bfast_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,894 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "bfast_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-09-03 06:23:39,894 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,896 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb.loc.sample' for 'blastdb' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,896 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'blastdb' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,896 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "blastdb", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-09-03 06:23:39,897 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb_p.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,898 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb_p.loc.sample' for 'blastdb_p' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,898 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'blastdb_p' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,898 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "blastdb_p", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-09-03 06:23:39,898 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/blastdb_d.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,899 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/blastdb_d.loc.sample' for 'blastdb_d' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,899 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'blastdb_d' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,900 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,900 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,900 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "bwa_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data WARNING 2024-09-03 06:23:39,901 [pN:job_handler_0,p:8,tN:MainThread] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,901 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_indexes_color' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,901 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "bwa_indexes_color", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-09-03 06:23:39,901 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/maf_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,903 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/maf_index.loc.sample' for 'indexed_maf_files' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,903 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'indexed_maf_files' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data INFO 2024-09-03 06:23:39,903 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/ngs_sim_fasta.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,904 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,904 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'ngs_sim_fasta' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,904 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "ngs_sim_fasta", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-09-03 06:23:39,905 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/perm_base_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,905 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,905 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'perm_base_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,905 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "perm_base_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-09-03 06:23:39,906 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/perm_color_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,906 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,906 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'perm_color_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,906 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "perm_color_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-09-03 06:23:39,907 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/picard_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,908 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/picard_index.loc.sample' for 'picard_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,908 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'picard_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,909 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "picard_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-09-03 06:23:39,909 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/picard_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,910 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/picard_index.loc.sample' for 'srma_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,910 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'srma_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,910 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "srma_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-09-03 06:23:39,910 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/mosaik_index.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,911 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,911 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'mosaik_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,911 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "mosaik_indexes", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-09-03 06:23:39,912 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/twobit.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,913 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/twobit.loc.sample' for 'twobit' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,913 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'twobit' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:39,913 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "twobit", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +charset_normalizer DEBUG 2024-09-03 06:23:40,053 [pN:job_handler_0,p:8,tN:MainThread] Encoding detection: utf_8 is most likely the one. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,053 [pN:job_handler_0,p:8,tN:MainThread] Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/galaxy/server/database/tmp/TTDT_URL_igv_broad_genomes-bwqmpv_i". +galaxy.tool_util.data WARNING 2024-09-03 06:23:40,058 [pN:job_handler_0,p:8,tN:MainThread] Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '' characters must be used to separate fields): + +galaxy.tool_util.data WARNING 2024-09-03 06:23:40,058 [pN:job_handler_0,p:8,tN:MainThread] Line 2 in tool data table 'igv_broad_genomes' is invalid (HINT: '' characters must be used to separate fields): +AccessDeniedAccess Denied8MTF678E7MXB7WEZw2UoxJqRZsWMAnldW2Py2pryGu3Hrv8aGGJLAywuEKboxDWFQ+uDZ1N/Vtfo6n9qYCqjhUgQM8UTjdHNseVcwgp9j6Hq3Vl1psNScCyuumk= +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,058 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tmp/TTDT_URL_igv_broad_genomes-bwqmpv_i' for 'igv_broad_genomes' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,059 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'igv_broad_genomes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-09-03 06:23:40,059 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/liftOver.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,060 [pN:job_handler_0,p:8,tN:MainThread] Loaded 0 lines from '/galaxy/server/database/tool-data/liftOver.loc.sample' for 'liftOver' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,060 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'liftOver' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,060 [pN:job_handler_0,p:8,tN:MainThread] While attempting to merge tool data table "liftOver", the other instance of the table specified that duplicate entries are not allowed, now deduplicating all previous entries. +galaxy.tool_util.data INFO 2024-09-03 06:23:40,061 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/bam_iobio.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,061 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/bam_iobio.loc.sample' for 'bam_iobio' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,061 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'bam_iobio' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-09-03 06:23:40,062 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/vcf_iobio.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,063 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,063 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'vcf_iobio' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-09-03 06:23:40,063 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/biom_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,064 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,064 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'biom_simple_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-09-03 06:23:40,064 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/intermine_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,065 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/intermine_simple_display.loc.sample' for 'intermine_simple_display' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,065 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'intermine_simple_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data INFO 2024-09-03 06:23:40,066 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/icn3d_simple_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,066 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/icn3d_simple_display.loc.sample' for 'icn3d_simple_display' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,067 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'icn3d_simple_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,067 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table '__dbkeys__'. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,067 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table '__dbkeys__'. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,067 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table '__dbkeys__' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,067 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'all_fasta'. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,067 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'all_fasta'. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,067 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'all_fasta' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,067 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'fasta_indexes'. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,067 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'fasta_indexes'. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,068 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'fasta_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,068 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bowtie2_indexes'. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,068 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bowtie2_indexes'. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,068 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bowtie2_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,068 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bwa_mem_indexes'. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,068 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'bwa_mem_indexes'. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,068 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'bwa_mem_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,068 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'hisat2_indexes'. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,068 [pN:job_handler_0,p:8,tN:MainThread] Encountered a file element () that does not contain a path value when loading tool data table 'hisat2_indexes'. +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,068 [pN:job_handler_0,p:8,tN:MainThread] Loading another instance of data table 'hisat2_indexes' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml', attempting to merge content. +galaxy.tool_util.data INFO 2024-09-03 06:23:40,069 [pN:job_handler_0,p:8,tN:MainThread] Could not find tool data /galaxy/server/database/tool-data/q2view_display.loc, reading sample +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,070 [pN:job_handler_0,p:8,tN:MainThread] Loaded 1 lines from '/galaxy/server/database/tool-data/q2view_display.loc.sample' for 'q2view_display' +galaxy.tool_util.data DEBUG 2024-09-03 06:23:40,070 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool data table 'q2view_display' from file '/galaxy/server/config/mutable/shed_tool_data_table_conf.xml' +galaxy.managers.dbkeys ERROR 2024-09-03 06:23:40,070 [pN:job_handler_0,p:8,tN:MainThread] ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/galaxy/server/database/tool-data/\n/cvmfs/data.galaxyproject.org/managed/location/builds.txt' +galaxy.util WARNING 2024-09-03 06:23:41,127 [pN:job_handler_0,p:8,tN:MainThread] directory not found: /galaxy/server/config/plugins/activities +galaxy.tools WARNING 2024-09-03 06:23:41,130 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:23:41,130 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:41,131 [pN:job_handler_0,p:8,tN:MainThread] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:23:41,181 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'genomespace/genomespace_importer.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:23:41,181 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'genomespace/genomespace_push.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:23:41,363 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:23:41,364 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:23:41,366 [pN:job_handler_0,p:8,tN:MainThread] Error reading tool from path: phenotype_association/sift.xml +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 881, in _load_tool_tag_set + tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 1108, in load_tool + tool = self.create_tool( + ^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 548, in create_tool + return self._create_tool_from_source(tool_source, config_file=config_file, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 564, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 356, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 821, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 818, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1143, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1428, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1623, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1636, in parse_param_elem + param = ToolParameter.build(self, input_source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 335, in build + return parameter_types[param_type](tool, input_source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2078, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1868, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 191, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 45, in from_element + return validator_types[_type].from_element(param, elem) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 399, in from_element + assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found" + ^^^^^^^^^^^^^^^^^^^^^^^^ +AssertionError: File /galaxy/server/database/tool-data/sift_db.loc specified by the 'filename' attribute not found +galaxy.tools WARNING 2024-09-03 06:23:41,401 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:23:41,401 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:41,413 [pN:job_handler_0,p:8,tN:MainThread] Tool path for shed tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml is /cvmfs/cloud.galaxyproject.org/tools +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,417 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_trim' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,422 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_removereads' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,427 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff_sars_cov_2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,436 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,441 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_filtervariants' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,445 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_getmasked' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,450 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ivar_variants' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,455 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,463 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_gtcheck' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,472 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fixploidy' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,480 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_convert_to_vcf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,491 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_norm' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,503 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_query_list_samples' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,509 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_missing2ref' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,518 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_cnv' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,529 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_setgt' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,539 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_counts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,548 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_mpileup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,564 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_mendelian' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,575 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_concat' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,583 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_convert_from_vcf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,597 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_impute_info' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,607 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_reheader' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,613 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_stats' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,627 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fill_an_ac' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,636 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_fill_tags' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,647 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_isec' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,656 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,665 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_roh' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,675 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,691 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,704 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,715 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_csq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,729 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_annotate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,739 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_dosage' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,749 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_query' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,760 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bcftools_plugin_tag2tag' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,770 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcf2tsv' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,776 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfaddinfo' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,781 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfallelicprimitives' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,786 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfannotate' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,790 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfannotategenotypes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,795 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfbedintersect' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,799 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfbreakcreatemulti' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,804 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfcheck' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,809 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfcombine' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,814 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfcommonsamples' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,819 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcffixup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,823 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfflatten' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,828 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfgeno2haplo' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,833 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfgenotypes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,837 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfhethom' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,841 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfleftalign' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,846 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfprimers' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,852 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfrandomsample' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,856 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfsort' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,860 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfvcfintersect' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,866 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfselectsamples' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,871 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfdistance' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,875 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcffilter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,882 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfdistance' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,886 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcftools_annotate' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,889 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcftools_slice' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,892 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'vcfallelicprimitives' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:41,896 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bedtools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,109 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bedtools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,339 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'collapse_collections' from owner 'nml' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,343 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'split_file_to_collection' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,354 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'collection_element_identifiers' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,356 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'collection_column_join' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,361 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_compute_matrix' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,374 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_heatmap' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,390 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_compare' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,399 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_pe_fragmentsize' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,405 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bigwig_compare' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,412 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_compute_gc_bias' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,419 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_correct_gc_bias' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,426 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_multi_bam_summary' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,438 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_multi_bigwig_summary' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,447 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_correlation' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,460 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_coverage' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,470 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_enrichment' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,481 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_fingerprint' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,492 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_pca' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,499 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_bam_coverage' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,509 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deeptools_plot_profile' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,519 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,540 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,552 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastqc' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,555 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'trimmomatic' from owner 'pjbriggs' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,564 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,590 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastqc' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,596 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,609 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,635 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,648 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'multiqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,663 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,675 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastqc' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,678 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sra_tools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,700 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ncbi_acc_download' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,707 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sra_tools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,731 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pygenometracks' from owner 'iuc' was not found in database. Tool will be loaded without install database. +:1: SyntaxWarning: invalid escape sequence '\d' +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,788 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'circos' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,886 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jbrowse' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.sanitize DEBUG 2024-09-03 06:23:42,916 [pN:job_handler_0,p:8,tN:MainThread] Invalid preset name specified: galaxy.util.mapped_chars +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,930 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'volcanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,935 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jbrowse' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.sanitize DEBUG 2024-09-03 06:23:42,968 [pN:job_handler_0,p:8,tN:MainThread] Invalid preset name specified: galaxy.util.mapped_chars +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,980 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pathview' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,988 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pathview' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:42,996 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,001 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,007 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'ggplot2_heatmap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,014 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'volcanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,020 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'minimap2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,031 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bowtie2' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,055 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwa' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,091 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwameth' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,095 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lastz' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,112 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,132 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rna_starsolo' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,154 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,169 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rgrnastar' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,194 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bwa' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,233 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_nucmer' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,241 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_mummerplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,248 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_show_coords' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,254 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_dnadiff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,263 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_mummer' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,273 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'mummer_delta_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,280 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_variant' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,290 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'flye' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,297 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_consensus_pipeline' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,305 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_variant_pipeline' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,314 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'medaka_consensus' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,321 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'nanoplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,329 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_events' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,335 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_hist' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,342 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_occupancy' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,348 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_qualpos' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,355 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_squiggle' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,361 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_yield_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,367 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'porechop' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,372 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_winner' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,378 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_times' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,383 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,388 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_stats' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,395 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_qualdist' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,401 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_nucdist' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,408 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'poretools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,414 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmon' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.basic WARNING 2024-09-03 06:23:43,425 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'fa', which is used in the 'format' attribute of parameter 'transcript' +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,430 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'kallisto_pseudo' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,436 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'kallisto_quant' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,444 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deseq2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,455 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'limma_voom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,464 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'edger' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,472 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sailfish' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,478 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'hisat2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,495 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'stringtie' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,512 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,522 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,528 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'limma_voom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,538 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'hisat2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,560 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deseq2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,573 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'hisat2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,588 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'featurecounts' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,595 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cufflinks' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,605 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deg_annotate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,610 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'goseq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,618 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'goseq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,626 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'deseq2' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,639 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'limma_voom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,648 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'egsea' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,657 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fgsea' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,661 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rseqc' from owner 'nilesh' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,791 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'rseqc' from owner 'nilesh' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,917 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pileup_interval' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,921 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qualimap_bamqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,931 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,946 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_reheader' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,951 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam_pileup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,955 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,962 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_split' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,966 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam2interval' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,969 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qualimap_multi_bamqc' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,974 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_phase' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,980 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,985 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_markdup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,991 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_fixmate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:43,995 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_fastx' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,008 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_depth' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,015 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_stats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,027 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_split' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,033 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_bedcov' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,039 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_calmd' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,046 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_idxstats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,051 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtool_filter2' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,056 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_flagstat' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,061 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_sort' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,067 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_mpileup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,077 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bam_to_sam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,082 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,091 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam_to_bam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,095 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_slice_bam' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,101 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_rmdup' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,107 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'filter_on_md' from owner 'boris' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,112 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sam_merge' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,115 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_stats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,125 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_phase' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,133 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_merge' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,140 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_markdup' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,149 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_idxstats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,156 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'bamtools_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,165 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,181 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_view' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,199 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'samtools_idxstats' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,206 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'revertr2orientationinbam' from owner 'lldelisle' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,209 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'filter_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,220 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'query_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,236 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_maker' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,241 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sqlite_to_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,251 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,254 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'concatenate_multiple_datasets' from owner 'mvdbeek' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,257 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'regex_find_replace' from owner 'galaxyp' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,265 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'table_compute' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,288 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'split_file_on_column' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,291 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'add_input_name_as_column' from owner 'mvdbeek' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,294 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,389 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'reshape2_melt' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,395 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'reshape2_cast' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,400 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,405 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gff3_rebase' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,411 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_remove_by_header' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,416 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_order_header_sort' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,419 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'replace_column_by_key_value_file' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,423 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,858 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'query_tabular' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,874 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,878 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'column_maker' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,886 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'table_compute' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:44,910 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,000 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,006 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'annotatemyids' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,010 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'text_processing' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,094 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'merge_cols' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,096 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'merge_cols' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,100 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,111 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_viterbi' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,117 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_indelqual' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,124 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,133 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_alnqual' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,140 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'freebayes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,161 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpsift_genesets' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,167 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpsift_dbnsfp' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,173 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,208 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpsift' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,250 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpfreqplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,254 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sniffles' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,259 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'jasminesv' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,267 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpfreqplot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,271 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,280 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'lofreq_call' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,290 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'freebayes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,306 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'freebayes' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,325 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,355 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'snpeff' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,374 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'diff' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,379 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'unicycler' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,386 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'spades' from owner 'nml' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,398 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'miniasm' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,402 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'racon' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,409 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sra_tools' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,431 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'pharmcat' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,437 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name '10x_bamtofastq' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,441 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_import' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,451 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_export' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,459 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_manipulate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,470 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'chromeister' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,476 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,485 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'modify_loom' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,492 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,499 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils_read_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-09-03 06:23:45,503 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0': a when tag has not been defined for 'add_metadata (add_metadata_file) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,504 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils_empty_drops' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,510 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspectclusters' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,529 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_filtnormconf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,542 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_clustering' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,554 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_trajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,567 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspecttrajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,579 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'alevin' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,592 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmonquantmerge' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,599 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'slice_image' from owner 'imgteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,603 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_create_qcmetric_ready_sce' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,609 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_tsne' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,614 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,622 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_normalize' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,627 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_dist_scatter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,632 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_exprs_freq' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,638 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_pca' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,643 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_cluster_reduce_dimension' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,662 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,679 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,702 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalize' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,715 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools DEBUG 2024-09-03 06:23:45,948 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1': a when tag has been defined for 'method (method) --> pl.rank_genes_groups_violin', but does not appear to be selectable. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,975 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_remove_confounders' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,985 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_parameter_iterator' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,990 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'droplet_barcode_plot' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:45,994 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_read_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,000 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gtf2gene_list' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,003 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmon_kallisto_mtx_to_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,007 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sceasy_convert' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,013 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_ops' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-09-03 06:23:46,019 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/0.0.3+galaxy0': a when tag has not been defined for 'copy_u (default) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,021 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'retrieve_scxa' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,024 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'music_inspect_eset' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tools.parameters.basic WARNING 2024-09-03 06:23:46,029 [pN:job_handler_0,p:8,tN:MainThread] Datatype class not found for extension 'rdata.eset', which is used in the 'format' attribute of parameter 'rds_eset' +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,030 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'music_construct_eset' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,037 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspectclusters' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,052 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_clustering' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,062 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_trajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,072 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_inspecttrajectory' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,082 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'alevin' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,094 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_create_qcmetric_ready_sce' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,099 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_filter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,104 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_dist_scatter' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,109 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scater_plot_pca' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,114 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tools DEBUG 2024-09-03 06:23:46,327 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0': a when tag has been defined for 'method (method) --> pl.rank_genes_groups_violin', but does not appear to be selectable. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,356 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_read_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,362 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'salmon_kallisto_mtx_to_10x' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,364 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_ops' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-09-03 06:23:46,370 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.6.0+galaxy1': a when tag has not been defined for 'copy_u (default) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,371 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_cells' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,380 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_cells' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,387 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,395 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_filter_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,403 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalise_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-09-03 06:23:46,409 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+3+galaxy0': a when tag has not been defined for 'exclude (exclude_highly_expressed) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,411 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_normalise_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-09-03 06:23:46,418 [pN:job_handler_0,p:8,tN:MainThread] Tool with id 'toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.6.0+galaxy0': a when tag has not been defined for 'exclude (exclude_highly_expressed) --> false', assuming empty inputs. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,420 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_variable_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,427 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_variable_genes' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,434 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_scale_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,441 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_scale_data' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,449 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_pca' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,455 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_pca' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,461 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_compute_graph' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,468 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_compute_graph' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,475 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_tsne' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,483 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_tsne' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,489 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_umap' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,497 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_run_umap' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,503 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_cluster' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,511 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_cluster' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,518 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_markers' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,525 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_find_markers' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,532 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot_embed' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,538 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot_embed' from owner 'ebi-gxa' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,546 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,556 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'dropletutils' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,563 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'raceid_filtnormconf' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,573 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'scanpy_plot' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,799 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_import' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,808 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_export' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,814 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_manipulate' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,822 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'anndata_inspect' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,833 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,866 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_filter' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,874 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_groomer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,881 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_manipulation' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,890 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fasta_compute_length' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,894 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_paired_end_deinterlacer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,898 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'fastq_paired_end_interlacer' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,904 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'flash' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,910 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'trim_galore' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,919 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,927 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,937 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,945 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,954 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:46,994 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_count' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,005 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'umi_tools_extract' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,017 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'seq_filter_by_id' from owner 'peterjc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,024 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,069 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'cutadapt' from owner 'lparsons' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,090 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'length_and_gc_content' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,096 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'length_and_gc_content' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,100 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_reverse' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,106 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_transpose' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,112 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_ops' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,123 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_transpose' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,129 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'datamash_transpose' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,134 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'picard' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,304 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'picard' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,462 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'picard' from owner 'devteam' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,616 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'map_param_value' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,622 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'compose_text_param' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,626 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gtftobed12' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,630 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_load' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,637 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_load' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,643 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_db_info' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,648 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_db_info' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,654 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_query' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,677 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'gemini_query' from owner 'iuc' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,684 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2_core__tools__export' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,698 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2_core__tools__import' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,729 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mafft_add' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,734 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mafft' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,738 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__alignment__mask' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,740 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__add_pseudocount' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,744 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__ancombc' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,749 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__tabulate' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,753 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__composition__ancom' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,757 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__trim_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,762 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__trim_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,766 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__demux_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,771 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__cutadapt__demux_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,777 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_pyro' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,782 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_ccs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,787 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,791 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__dada2__denoise_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,796 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__denoise_16s' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,801 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__denoise_other' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,806 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__deblur__visualize_stats' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,810 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__emp_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,816 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__subsample_paired' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,820 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__subsample_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,824 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,828 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__filter_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,832 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__demux__emp_single' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,836 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_correlation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,841 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__adonis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,845 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__umap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,848 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__pcoa' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,851 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__bioenv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,854 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__pcoa_biplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,858 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__tsne' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,862 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_group_significance' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,867 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__procrustes_analysis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,872 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__mantel' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,877 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,881 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_group_significance' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,885 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__core_metrics_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,892 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__core_metrics' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,897 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_correlation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,901 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__filter_distance_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,906 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,910 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,914 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,917 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__alpha_rarefaction' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,921 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity__beta_rarefaction' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,927 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__observed_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,931 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__bray_curtis' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,934 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,939 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__alpha_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,942 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__shannon_entropy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,947 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__jaccard' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,951 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__pielou_evenness' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,954 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_phylogenetic_meta_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,958 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__weighted_unifrac' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,962 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__unweighted_unifrac' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,967 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__beta_phylogenetic_passthrough' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,972 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__diversity_lib__faith_pd' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,976 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__procrustes_plot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,980 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__plot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,984 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__emperor__biplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,989 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,993 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__fit_classifier_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:47,997 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__fit_classifier_naive_bayes' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,004 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_consensus_blast' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,009 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__extract_reads' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,014 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_hybrid_vsearch_sklearn' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,020 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__classify_consensus_vsearch' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,025 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__blast' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,030 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__find_consensus_annotation' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,035 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_classifier__vsearch_global' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,041 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__tabulate_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,045 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__presence_absence' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,048 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,054 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,058 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_features_conditionally' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,061 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__rename_ids' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,065 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,069 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__relative_frequency' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,073 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,077 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,082 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__rarefy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,086 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__transpose' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,089 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__subsample' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,092 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__heatmap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,099 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__merge_taxa' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,103 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__core_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,107 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__group' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,112 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__feature_table__filter_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,117 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__sepp' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,122 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__classify_otus_experimental' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,127 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__fragment_insertion__filter_features' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,132 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_phylogenetic' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,136 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__correlation_clustering' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,140 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__dendrogram_heatmap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,145 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__gradient_clustering' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,150 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_phylogenetic_ordination' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,153 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__assign_ids' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,157 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_phylogenetic_differential' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,161 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__gneiss__ilr_hierarchical' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,164 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__pairwise_distances' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,170 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__feature_volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,177 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__nmit' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,180 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__first_differences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,186 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__plot_feature_volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,192 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__first_distances' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,196 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__linear_mixed_effects' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,204 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__volatility' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,210 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__pairwise_differences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,217 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__anova' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,222 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__longitudinal__maturity_index' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,230 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__shuffle_groups' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,235 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__distance_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,238 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__metadata__tabulate' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,242 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__raxml_rapid_bootstrap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,246 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__fasttree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,250 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_iqtree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,260 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__iqtree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,268 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__robinson_foulds' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,272 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_raxml' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,276 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__filter_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,281 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__midpoint_root' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,285 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__align_to_tree_mafft_fasttree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,290 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__raxml' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,294 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__filter_tree' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,299 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__phylogeny__iqtree_ultrafast_bootstrap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,307 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_composition' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,313 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,317 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__filter_reads' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,321 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__bowtie2_build' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,325 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__evaluate_taxonomy' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,330 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_control__exclude_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,335 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__quality_filter__q_score' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,340 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__metatable' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,344 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__fit_classifier' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,349 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__regress_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,353 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,359 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__scatterplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,363 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples_from_dist' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,368 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__confusion_matrix' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,372 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__split_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,377 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__summarize' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,379 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__heatmap' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,386 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__classify_samples_ncv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,391 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__fit_regressor' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,397 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__predict_classification' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,400 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__regress_samples_ncv' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,404 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__sample_classifier__predict_regression' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,409 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__collapse' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,413 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__filter_table' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,418 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__barplot' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,422 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__taxa__filter_seqs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,427 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_closed_reference' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,432 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_open_reference' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,438 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__merge_pairs' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,442 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__uchime_denovo' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,446 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__dereplicate_sequences' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,451 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__fastq_stats' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,455 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__uchime_ref' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,459 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'qiime2__vsearch__cluster_features_de_novo' from owner 'q2d2' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,463 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_build_pipeline' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,527 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_build_pipeline' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,580 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_searchcv' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,636 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_searchcv' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,677 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'plotly_parallel_coordinates_plot' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,680 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'plotly_parallel_coordinates_plot' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,684 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_ensemble' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,726 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'sklearn_ensemble' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tool_util.toolbox.base WARNING 2024-09-03 06:23:48,770 [pN:job_handler_0,p:8,tN:MainThread] Attempted to load tool shed tool, but the repository with name 'plotly_regression_performance_plots' from owner 'bgruening' was not found in database. Tool will be loaded without install database. +galaxy.tools WARNING 2024-09-03 06:23:48,774 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:23:48,774 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:23:48,774 [pN:job_handler_0,p:8,tN:MainThread] Shed-enabled tool configuration file does not exist, but will be created on demand: /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tools WARNING 2024-09-03 06:23:48,774 [pN:job_handler_0,p:8,tN:MainThread] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:23:48,774 [pN:job_handler_0,p:8,tN:MainThread] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,774 [pN:job_handler_0,p:8,tN:MainThread] Tool path for shed tool configuration /galaxy/server/config/migrated_tools_conf.xml is /galaxy/server/database/shed_tools +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,774 [pN:job_handler_0,p:8,tN:MainThread] Reading tools from config files finished (7645.301 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,775 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,775 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,775 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,775 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,776 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,777 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,778 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,779 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,780 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,781 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,782 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,783 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,784 [pN:job_handler_0,p:8,tN:MainThread] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,784 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,785 [pN:job_handler_0,p:8,tN:MainThread] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,785 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,786 [pN:job_handler_0,p:8,tN:MainThread] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,786 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,787 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,788 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,788 [pN:job_handler_0,p:8,tN:MainThread] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,789 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,790 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,791 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,792 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,793 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,794 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,795 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,796 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,796 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,797 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,798 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,799 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,800 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,801 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,801 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,802 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,803 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,804 [pN:job_handler_0,p:8,tN:MainThread] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,804 [pN:job_handler_0,p:8,tN:MainThread] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,804 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,805 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,806 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,806 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,806 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,807 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,808 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,809 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,810 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,810 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,810 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,811 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,812 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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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 2024-09-03 06:23:48,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6, version: 0.0.1+galaxy6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/sceasy_convert/sceasy_convert/0.0.5+galaxy1, version: 0.0.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/0.0.3+galaxy0, version: 0.0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,813 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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DEBUG 2024-09-03 06:23:48,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,822 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,823 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_de_novo/qiime2__vsearch__cluster_features_de_novo/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 2024-09-03 06:23:48,832 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Machine Learning +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1, version: 1.0.8.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0, version: 1.0.11.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,832 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.2, version: 0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,833 [pN:job_handler_0,p:8,tN:MainThread] Loading section: RSeQC +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,833 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,833 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,833 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,833 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,833 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:48,833 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:48,834 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:48,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,834 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:48,834 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:48,834 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:48,834 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,834 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,834 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,834 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,834 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,tN:MainThread] Loading section: MiModD +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Du Novo +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Seqtk +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,tN:MainThread] Loading section: TRANSIT +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Statistics +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,835 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,836 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,837 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,837 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,837 [pN:job_handler_0,p:8,tN:MainThread] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,837 [pN:job_handler_0,p:8,tN:MainThread] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,837 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,837 [pN:job_handler_0,p:8,tN:MainThread] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,837 [pN:job_handler_0,p:8,tN:MainThread] Loading tool panel finished (62.167 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,843 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,844 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,845 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,846 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,847 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,848 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,849 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,850 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,851 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,852 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,853 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,854 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,855 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,856 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,857 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,858 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,859 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,860 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,861 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,862 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,863 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,864 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,865 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,866 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,867 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,868 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,869 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,870 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,871 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,872 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,873 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,874 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,875 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,876 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,877 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,878 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,878 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,878 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,878 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,878 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,878 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,878 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,878 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,878 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,878 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,878 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,879 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, version: 1.7.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0, version: 0.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2, version: 1.6.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,880 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,892 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,892 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_group_significance/qiime2__diversity__alpha_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,892 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics_phylogenetic/qiime2__diversity__core_metrics_phylogenetic/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,893 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__core_metrics/qiime2__diversity__core_metrics/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,893 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__alpha_correlation/qiime2__diversity__alpha_correlation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,893 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__filter_distance_matrix/qiime2__diversity__filter_distance_matrix/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,893 [pN:job_handler_0,p:8,tN:MainThread] Loaded 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,907 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0, version: 1.0.11.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,907 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,907 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.2, version: 0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,907 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,908 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,908 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,908 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,908 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,908 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,908 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:48,908 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:48,908 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:48,909 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,909 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:48,909 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:48,909 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:48,909 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,909 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,909 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,909 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,909 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,909 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,910 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,910 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,910 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,910 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,910 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,910 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,910 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,910 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,910 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,910 [pN:job_handler_0,p:8,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 2024-09-03 06:23:48,911 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,911 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,911 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,911 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,911 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-09-03 06:23:48,911 [pN:job_handler_0,p:8,tN:MainThread] Loading EDAM tool panel finished (73.811 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,919 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,920 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,920 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,920 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,920 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,920 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,920 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,920 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,921 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,921 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,921 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,921 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,922 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,922 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,922 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,922 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,922 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,922 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,922 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,922 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,922 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,922 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,923 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,923 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,923 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,923 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,923 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,923 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,923 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,923 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,923 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,924 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,924 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,924 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,924 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,924 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,924 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,924 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,924 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,924 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,925 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,925 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,925 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,925 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,926 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,926 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,926 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,926 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,926 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,926 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,927 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,927 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,927 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,927 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,927 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,928 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,928 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,928 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,928 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,928 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,929 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,930 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,930 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,930 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,930 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,930 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,930 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,930 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,930 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,930 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,930 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,930 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,930 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,931 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,931 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,931 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,931 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,931 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,931 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,931 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,931 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,931 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,931 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,931 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,931 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,932 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,932 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,932 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,932 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,932 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,932 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,932 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,932 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,932 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,932 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,932 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,933 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,933 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,933 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,933 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,933 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,933 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,933 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,933 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,933 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,933 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,933 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,933 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,934 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,934 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,934 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,934 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,934 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,934 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,934 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,934 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,934 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,934 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,934 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,934 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,934 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,935 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,935 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,935 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,935 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,935 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,935 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,935 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,935 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,935 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,935 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,935 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,936 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,936 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,936 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,936 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,936 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,936 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,936 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,936 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,936 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,936 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,936 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,936 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,937 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,937 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,937 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,937 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,937 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,937 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,937 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,937 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,938 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,938 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,938 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,938 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,938 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,938 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,938 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,938 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,938 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,939 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,939 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,939 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,939 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,939 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,939 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,939 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,939 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,939 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,939 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,940 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,940 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,940 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,940 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,940 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,940 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,940 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,941 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,941 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,941 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,941 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,941 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,941 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,941 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,942 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,942 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,942 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,942 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,942 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,942 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,942 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,942 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,942 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,943 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,943 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,943 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,943 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,943 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,943 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,943 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,943 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,943 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,943 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,944 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,944 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,944 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,944 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,944 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,944 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,944 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,944 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,944 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,944 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,945 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,945 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,945 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,945 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,945 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,945 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,945 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,945 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,946 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,946 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,946 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,946 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,946 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,946 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,946 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,946 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,946 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,947 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,947 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,947 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,947 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,947 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,947 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,947 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,947 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,947 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,947 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,948 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,948 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,948 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,948 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,948 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,948 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,948 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,948 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,948 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,948 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,948 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,949 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,949 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,949 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,949 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,949 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,949 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,949 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,949 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,949 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,949 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,949 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,950 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,950 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,950 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,950 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,950 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,950 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,950 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,950 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,950 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,950 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,950 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,951 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,952 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,953 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,954 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,955 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,956 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,957 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,958 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,958 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,958 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,958 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,958 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,958 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,958 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,958 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,958 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,958 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,958 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,958 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,958 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,959 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,959 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,959 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,959 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,959 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,959 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,959 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,959 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,959 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,959 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,959 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,959 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,959 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,960 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,960 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,960 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,960 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,960 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,960 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,960 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,960 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,960 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,960 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,961 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,961 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,961 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,961 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,961 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,961 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,961 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,961 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,961 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,961 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,961 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,961 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,962 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,962 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,962 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,962 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,962 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,962 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,962 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,962 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,962 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,962 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,962 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,963 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,963 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,963 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,963 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,963 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,963 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,963 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,963 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,963 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,963 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,963 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,964 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,964 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,964 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,964 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,964 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,964 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,964 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,964 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,964 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,964 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,964 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,964 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,965 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,965 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,965 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,965 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,965 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,965 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,965 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,966 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,966 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,966 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,966 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,967 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,967 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,967 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,967 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,967 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,967 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,967 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,967 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,967 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,967 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,968 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,968 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,968 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,968 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,968 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,968 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,968 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,968 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,968 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,969 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,969 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,969 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,969 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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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 2024-09-03 06:23:48,970 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6, version: 0.0.1+galaxy6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,970 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/sceasy_convert/sceasy_convert/0.0.5+galaxy1, version: 0.0.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,970 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/0.0.3+galaxy0, version: 0.0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,970 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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DEBUG 2024-09-03 06:23:48,984 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,984 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,984 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,984 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__dereplicate_sequences/qiime2__vsearch__dereplicate_sequences/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 2024-09-03 06:23:48,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__fastq_stats/qiime2__vsearch__fastq_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 2024-09-03 06:23:48,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__uchime_ref/qiime2__vsearch__uchime_ref/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 2024-09-03 06:23:48,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_de_novo/qiime2__vsearch__cluster_features_de_novo/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 2024-09-03 06:23:48,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1, version: 1.0.8.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0, version: 1.0.11.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:48,999 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,000 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.2, version: 0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,000 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,000 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,000 [pN:job_handler_0,p:8,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 2024-09-03 06:23:49,000 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,000 [pN:job_handler_0,p:8,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 2024-09-03 06:23:49,000 [pN:job_handler_0,p:8,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 2024-09-03 06:23:49,000 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:49,000 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:49,000 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:49,000 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,000 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:49,001 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:49,001 [pN:job_handler_0,p:8,tN:MainThread] 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 2024-09-03 06:23:49,001 [pN:job_handler_0,p:8,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 2024-09-03 06:23:49,001 [pN:job_handler_0,p:8,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 2024-09-03 06:23:49,001 [pN:job_handler_0,p:8,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 2024-09-03 06:23:49,001 [pN:job_handler_0,p:8,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 2024-09-03 06:23:49,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,001 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,002 [pN:job_handler_0,p:8,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 2024-09-03 06:23:49,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,002 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,003 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,003 [pN:job_handler_0,p:8,tN:MainThread] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:23:49,003 [pN:job_handler_0,p:8,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-09-03 06:23:49,003 [pN:job_handler_0,p:8,tN:MainThread] Loading EDAM tool panel finished (91.540 ms) +galaxy.tool_util.toolbox.integrated_panel DEBUG 2024-09-03 06:23:49,003 [pN:job_handler_0,p:8,tN:MainThread] Writing integrated tool panel config file to '/galaxy/server/config/mutable/integrated_tool_panel.xml' +galaxy.tool_util.deps WARNING 2024-09-03 06:23:49,014 [pN:job_handler_0,p:8,tN:MainThread] Path '/galaxy/server/database/deps' does not exist, ignoring +galaxy.tool_util.deps WARNING 2024-09-03 06:23:49,014 [pN:job_handler_0,p:8,tN:MainThread] Path '/galaxy/server/database/deps' is not directory, ignoring +galaxy.tool_util.deps.installable WARNING 2024-09-03 06:23:49,024 [pN:job_handler_0,p:8,tN:MainThread] Conda not installed and auto-installation disabled. +galaxy.tool_util.deps.installable WARNING 2024-09-03 06:23:49,028 [pN:job_handler_0,p:8,tN:MainThread] Conda not installed and auto-installation disabled. +galaxy.tool_util.deps.containers DEBUG 2024-09-03 06:23:49,037 [pN:job_handler_0,p:8,tN:MainThread] Loading container resolution config from file '/galaxy/server/config/container_resolvers_conf.xml' +galaxy.tools.search WARNING 2024-09-03 06:23:49,041 [pN:job_handler_0,p:8,tN:MainThread] Index at '/galaxy/server/database/tool_search_index/default' uses outdated schema, creating a new index +galaxy.tools.search WARNING 2024-09-03 06:23:49,057 [pN:job_handler_0,p:8,tN:MainThread] Index at '/galaxy/server/database/tool_search_index/ontology:edam_operations' uses outdated schema, creating a new index +galaxy.tools.search WARNING 2024-09-03 06:23:49,075 [pN:job_handler_0,p:8,tN:MainThread] Index at '/galaxy/server/database/tool_search_index/ontology:edam_topics' uses outdated schema, creating a new index +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,092 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,092 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,093 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,093 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,094 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,094 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bed' for datatype 'bed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,094 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,096 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,096 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,098 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,099 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,099 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,100 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'intermine_simple' for datatype 'intermine_tabular', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,101 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,102 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,103 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,103 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,104 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,106 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,106 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,107 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,107 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'avivator' for datatype 'tiff', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,107 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'avivator' for datatype 'ome.tiff', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,108 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'q2view' for datatype 'qza', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,108 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'q2view' for datatype 'qzv', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,110 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,110 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'minerva_tabular' for datatype 'tabular', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,112 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,113 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,113 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,114 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,114 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igb_wig' for datatype 'wig', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,115 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,115 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'igv_genbank' for datatype 'genbank', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'sdf', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,116 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'mol2', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,117 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'icn3d_simple' for datatype 'pdb', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,118 [pN:job_handler_0,p:8,tN:MainThread] Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,118 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,118 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,118 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,118 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,118 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,118 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,118 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,118 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,118 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,118 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,118 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,118 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,118 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'probed' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,119 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'fasta.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,120 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'a3m' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,120 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,120 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,120 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,120 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,120 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.bz2' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,120 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.bz2' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,120 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,120 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,121 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,121 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,121 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,121 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,122 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'sequences' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,122 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,122 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,122 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,122 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'interval_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,122 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,122 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,122 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,122 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'juicer_medium_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,123 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,123 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,123 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,123 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'bed_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,123 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'ensembl_interval' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,123 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,123 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'rviewer_interval' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,123 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'gff_tabix.gz' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,124 [pN:job_handler_0,p:8,tN:MainThread] Adding inherited display application 'igv_fasta' to datatype 'mothur.align' +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,128 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,129 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,131 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,132 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,133 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,134 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,135 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,135 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,137 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,137 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,138 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,139 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,140 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,141 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,142 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,143 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,144 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,145 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,147 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,148 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,149 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,151 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,152 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,153 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,154 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,155 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,156 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,157 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,158 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,159 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,160 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,161 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,162 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,163 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,164 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,164 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,166 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,167 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,168 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,169 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,170 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,171 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,172 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,172 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,174 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,175 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,176 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,177 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,178 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,179 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,180 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,181 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,182 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,183 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,184 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,185 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,185 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,186 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,187 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,189 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,191 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,192 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,193 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,194 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,194 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,196 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,196 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,197 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,198 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,199 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,201 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,202 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,203 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,204 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,205 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,206 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,207 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,208 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,209 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,210 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,212 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,213 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,214 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,215 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,216 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,217 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,218 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,219 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,221 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,222 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,223 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,224 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,225 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,226 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,226 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,227 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,229 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,229 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,231 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,232 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,233 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,234 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,235 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,236 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,237 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,238 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,239 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,240 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,240 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,241 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,242 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,243 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,245 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,246 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,247 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,248 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,249 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,251 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,252 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,253 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,254 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,256 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,257 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,258 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,260 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,261 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,263 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,264 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,265 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,266 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,268 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,269 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,270 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,272 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,273 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,275 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,276 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,278 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,279 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,281 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,281 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,283 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,284 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,285 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,287 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,288 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,289 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,290 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,291 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,292 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,293 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,294 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,295 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,296 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,297 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,297 [pN:job_handler_0,p:8,tN:MainThread] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-09-03 06:23:49,299 [pN:job_handler_0,p:8,tN:MainThread] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-09-03 06:23:49,300 [pN:job_handler_0,p:8,tN:MainThread] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-09-03 06:23:49,301 [pN:job_handler_0,p:8,tN:MainThread] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-09-03 06:23:49,302 [pN:job_handler_0,p:8,tN:MainThread] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-09-03 06:23:49,303 [pN:job_handler_0,p:8,tN:MainThread] Loaded data fetch tool: __DATA_FETCH__ +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,304 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: PCA_3Dplot +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,305 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,306 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image +galaxy.visualization.plugins.config_parser INFO 2024-09-03 06:23:49,306 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,306 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz +galaxy.visualization.plugins.config_parser INFO 2024-09-03 06:23:49,307 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,307 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: csg +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,308 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,309 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,309 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: editor +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,310 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: example +galaxy.visualization.plugins.config_parser INFO 2024-09-03 06:23:49,310 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,310 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: fits_image_viewer +galaxy.visualization.plugins.config_parser INFO 2024-09-03 06:23:49,311 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,311 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,312 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: h5web +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,314 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,316 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_default +galaxy.visualization.plugins.config_parser INFO 2024-09-03 06:23:49,317 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,317 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace +galaxy.visualization.plugins.config_parser INFO 2024-09-03 06:23:49,317 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,317 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,320 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,322 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,324 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,327 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,329 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter +galaxy.visualization.plugins.config_parser INFO 2024-09-03 06:23:49,330 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,330 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: audio_player +galaxy.visualization.plugins.config_parser INFO 2024-09-03 06:23:49,330 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,330 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: video_player +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,331 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: msa +galaxy.visualization.plugins.config_parser INFO 2024-09-03 06:23:49,332 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,332 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,333 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,334 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nora +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,336 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,339 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,341 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,344 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,346 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,348 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,351 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,353 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,355 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,357 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,359 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,361 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,364 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,365 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,366 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,367 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,368 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: pv +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,368 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,369 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: tiffviewer +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,370 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,371 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: ts_visjs +galaxy.visualization.plugins.config_parser INFO 2024-09-03 06:23:49,371 [pN:job_handler_0,p:8,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,371 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept +galaxy.visualization.plugins.registry INFO 2024-09-03 06:23:49,372 [pN:job_handler_0,p:8,tN:MainThread] VisualizationsRegistry, loaded plugin: venn +galaxy.tours._impl INFO 2024-09-03 06:23:49,389 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.galaxy_ui' +galaxy.tours._impl INFO 2024-09-03 06:23:49,400 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.deferred' +galaxy.tours._impl INFO 2024-09-03 06:23:49,408 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.windows' +galaxy.tours._impl INFO 2024-09-03 06:23:49,418 [pN:job_handler_0,p:8,tN:MainThread] Loaded tour 'core.history' +galaxy.jobs.manager DEBUG 2024-09-03 06:23:49,423 [pN:job_handler_0,p:8,tN:MainThread] Initializing job handler +galaxy.jobs INFO 2024-09-03 06:23:49,423 [pN:job_handler_0,p:8,tN:MainThread] Handler 'job_handler_0' will load all configured runner plugins +galaxy.jobs.runners DEBUG 2024-09-03 06:23:49,425 [pN:job_handler_0,p:8,tN:MainThread] Loading KubernetesRunner with params: {'k8s_cleanup_job': 'onsuccess', 'k8s_data_volume_claim': 'edge-24-09-03-06-11-1-galaxy-galaxy-pvc:/galaxy/server/database', 'k8s_fs_group_id': '101', 'k8s_galaxy_instance_id': 'edge-24-09-03-06-11-1-galaxy', 'k8s_interactivetools_ingress_annotations': '\nnginx.ingress.kubernetes.io/auth-tls-pass-certificate-to-upstream: "true"\nnginx.ingress.kubernetes.io/auth-tls-secret: \'edge-24-09-03-06-11-1/ca-secret\'\nnginx.ingress.kubernetes.io/auth-tls-verify-client: "on"\nnginx.ingress.kubernetes.io/auth-tls-verify-depth: "1"\nnginx.ingress.kubernetes.io/proxy-body-size: 10G\nnginx.ingress.kubernetes.io/proxy-read-timeout: "600"\nnginx.ingress.kubernetes.io/ssl-redirect: "true"\n', 'k8s_interactivetools_use_ssl': True, 'k8s_job_ttl_secs_after_finished': 90, 'k8s_namespace': 'edge-24-09-03-06-11-1', 'k8s_node_selector': 'cloud.google.com/gke-nodepool: default-pool', 'k8s_persistent_volume_claims': 'edge-24-09-03-06-11-1-galaxy-galaxy-pvc/config:/galaxy/server/database/config:r,edge-24-09-03-06-11-1-galaxy-galaxy-pvc/tmp:/galaxy/server/database/tmp:rw,edge-24-09-03-06-11-1-galaxy-galaxy-pvc/tool-data:/galaxy/server/database/tool-data:rw,edge-24-09-03-06-11-1-galaxy-galaxy-pvc/tools:/galaxy/server/database/tools:r,edge-24-09-03-06-11-1-galaxy-galaxy-pvc/shed_tools:/galaxy/server/database/shed_tools:r,edge-24-09-03-06-11-1-galaxy-refdata-gxy-pvc/data.galaxyproject.org:/cvmfs/data.galaxyproject.org:r,edge-24-09-03-06-11-1-galaxy-galaxy-pvc/cvmfsclone:/cvmfs/cloud.galaxyproject.org:r', 'k8s_pod_priority_class': 'edge-24-09-03-06-11-1-priority-class', 'k8s_pull_policy': 'IfNotPresent', 'k8s_supplemental_group_id': '101', 'k8s_use_service_account': True, 'k8s_working_volume_claim': 'edge-24-09-03-06-11-1-galaxy-galaxy-pvc:/galaxy/server/database'} +galaxy.jobs.runners.state_handler_factory DEBUG 2024-09-03 06:23:49,426 [pN:job_handler_0,p:8,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners.util.pykube_util ERROR 2024-09-03 06:23:49,427 [pN:job_handler_0,p:8,tN:MainThread] Galaxy instance [edge-24-09-03-06-11-1-galaxy] is either too long (>20 characters) or it includes non DNS acceptable characters, ignoring it. +galaxy.jobs DEBUG 2024-09-03 06:23:49,427 [pN:job_handler_0,p:8,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.kubernetes:KubernetesJobRunner' as 'k8s' +galaxy.jobs.runners.state_handler_factory DEBUG 2024-09-03 06:23:49,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs DEBUG 2024-09-03 06:23:49,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' +galaxy.jobs.handler DEBUG 2024-09-03 06:23:49,428 [pN:job_handler_0,p:8,tN:MainThread] Loaded job runners plugins: k8s:local +galaxy.jobs.runners DEBUG 2024-09-03 06:23:49,439 [pN:job_handler_0,p:8,tN:MainThread] Starting 4 KubernetesRunner workers +galaxy.jobs.runners DEBUG 2024-09-03 06:23:49,441 [pN:job_handler_0,p:8,tN:MainThread] Starting 4 LocalRunner workers +galaxy.jobs.handler DEBUG 2024-09-03 06:23:49,442 [pN:job_handler_0,p:8,tN:MainThread] Handler queue starting for jobs assigned to handler: job_handler_0 +galaxy.jobs.handler INFO 2024-09-03 06:23:49,452 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Handler job grabber initialized with 'db-skip-locked' assignment method for handler 'job_handler_0', tag(s): _default_ +galaxy.jobs.handler INFO 2024-09-03 06:23:49,454 [pN:job_handler_0,p:8,tN:MainThread] job handler queue started +galaxy.jobs.handler INFO 2024-09-03 06:23:49,454 [pN:job_handler_0,p:8,tN:MainThread] job handler stop queue started +galaxy.web_stack.handlers DEBUG 2024-09-03 06:23:49,458 [pN:job_handler_0,p:8,tN:MainThread] Read definition for handler 'workflow_scheduler0' +galaxy.web_stack.handlers DEBUG 2024-09-03 06:23:49,458 [pN:job_handler_0,p:8,tN:MainThread] Read definition for handler 'workflow_scheduler0' +galaxy.web_stack.handlers DEBUG 2024-09-03 06:23:49,459 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'schedulers' +galaxy.web_stack.handlers INFO 2024-09-03 06:23:49,473 [pN:job_handler_0,p:8,tN:MainThread] WorkflowSchedulingManager: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on to override the default +galaxy.workflow.scheduling_manager INFO 2024-09-03 06:23:49,473 [pN:job_handler_0,p:8,tN:MainThread] Workflow scheduling handler assignment method(s): db-skip-locked +galaxy.workflow.scheduling_manager INFO 2024-09-03 06:23:49,473 [pN:job_handler_0,p:8,tN:MainThread] Tag [schedulers] handlers: workflow_scheduler0 +galaxy.web_stack.handlers DEBUG 2024-09-03 06:23:49,473 [pN:job_handler_0,p:8,tN:MainThread] default set to child with id or tag 'schedulers' +galaxy.queue_worker INFO 2024-09-03 06:23:49,479 [pN:job_handler_0,p:8,tN:MainThread] Binding and starting galaxy control worker for job_handler_0 +galaxy.queue_worker INFO 2024-09-03 06:23:49,480 [pN:job_handler_0,p:8,tN:MainThread] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.model.database_heartbeat DEBUG 2024-09-03 06:23:49,872 [pN:job_handler_0,p:8,tN:database_heartbeart_job_handler_0.thread] job_handler_0 is config watcher +galaxy.app INFO 2024-09-03 06:23:49,893 [pN:job_handler_0,p:8,tN:MainThread] Galaxy app startup finished (11816.286 ms) +galaxy.web_stack INFO 2024-09-03 06:23:49,893 [pN:job_handler_0,p:8,tN:MainThread] Galaxy server instance 'job_handler_0' is running +galaxy.queue_worker INFO 2024-09-03 06:23:49,903 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker DEBUG 2024-09-03 06:23:49,903 [pN:job_handler_0,p:8,tN:Thread-1] App is not a webapp, not building a search index +galaxy.queue_worker INFO 2024-09-03 06:24:08,894 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'reload_toolbox' task, executing now. +galaxy.queue_worker DEBUG 2024-09-03 06:24:08,894 [pN:job_handler_0,p:8,tN:Thread-1] Executing toolbox reload on 'job_handler_0' +galaxy.util WARNING 2024-09-03 06:24:08,914 [pN:job_handler_0,p:8,tN:Thread-1] directory not found: /galaxy/server/config/plugins/activities +galaxy.tools WARNING 2024-09-03 06:24:08,918 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:24:08,919 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,919 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:24:08,920 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_importer.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:24:08,920 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_push.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:24:08,922 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:24:08,922 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:24:08,923 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool from path: phenotype_association/sift.xml +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 881, in _load_tool_tag_set + tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 1108, in load_tool + tool = self.create_tool( + ^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 548, in create_tool + return self._create_tool_from_source(tool_source, config_file=config_file, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 564, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 356, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 821, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 818, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1143, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1428, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1623, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1636, in parse_param_elem + param = ToolParameter.build(self, input_source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 335, in build + return parameter_types[param_type](tool, input_source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2078, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1868, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 191, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 45, in from_element + return validator_types[_type].from_element(param, elem) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 399, in from_element + assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found" + ^^^^^^^^^^^^^^^^^^^^^^^^ +AssertionError: File /galaxy/server/database/tool-data/sift_db.loc specified by the 'filename' attribute not found +galaxy.tools WARNING 2024-09-03 06:24:08,925 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:24:08,925 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,939 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml is /cvmfs/cloud.galaxyproject.org/tools +galaxy.tools WARNING 2024-09-03 06:24:08,975 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:24:08,975 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:24:08,975 [pN:job_handler_0,p:8,tN:Thread-1] Shed-enabled tool configuration file does not exist, but will be created on demand: /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tools WARNING 2024-09-03 06:24:08,975 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:24:08,975 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,976 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /galaxy/server/config/migrated_tools_conf.xml is /galaxy/server/database/shed_tools +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,976 [pN:job_handler_0,p:8,tN:Thread-1] Reading tools from config files finished (57.502 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,976 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,976 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,977 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,978 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,979 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,979 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,980 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,981 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,982 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,983 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,984 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,985 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,985 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,986 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,986 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,987 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,987 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,987 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,987 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,987 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,987 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,987 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,987 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,988 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,989 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,990 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,991 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,991 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,992 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,993 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,994 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,995 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,996 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,996 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,997 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,998 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:08,999 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,000 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,001 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,002 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,003 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,004 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,005 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,005 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,005 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,006 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,006 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,007 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,008 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,009 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,009 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,009 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,010 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,011 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,011 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,011 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,012 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,012 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,012 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,012 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,012 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,012 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,012 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,012 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,013 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,014 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,015 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,015 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,015 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,016 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,017 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,017 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,017 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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2024-09-03 06:24:09,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,025 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta/qiime2__diversity__beta/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,026 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__dereplicate_sequences/qiime2__vsearch__dereplicate_sequences/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 2024-09-03 06:24:09,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__fastq_stats/qiime2__vsearch__fastq_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 2024-09-03 06:24:09,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__uchime_ref/qiime2__vsearch__uchime_ref/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 2024-09-03 06:24:09,035 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,036 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RSeQC +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,036 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,036 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,037 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,037 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,037 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,037 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,037 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: MiModD +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Du Novo +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Seqtk +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: TRANSIT +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Statistics +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,038 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,039 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,040 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,040 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,040 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,040 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,040 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,040 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,041 [pN:job_handler_0,p:8,tN:Thread-1] Loading tool panel finished (64.716 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,047 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,048 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,049 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,050 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,051 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,052 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,053 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,054 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,055 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,056 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,057 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,058 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,059 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,060 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,061 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,062 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,063 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,064 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,065 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,066 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,067 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,068 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,069 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,070 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,071 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,072 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,073 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,074 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,074 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,075 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,076 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,077 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,078 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,079 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,080 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,081 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,082 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,083 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,084 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,085 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,086 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,087 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2, version: 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, version: 1.7.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,088 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0, version: 0.0.1+galaxy0 into tool panel.... 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version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,097 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,098 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,098 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,098 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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DEBUG 2024-09-03 06:24:09,100 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__blast/qiime2__feature_classifier__blast/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,101 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__find_consensus_annotation/qiime2__feature_classifier__find_consensus_annotation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,101 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__vsearch_global/qiime2__feature_classifier__vsearch_global/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0, version: 1.0.11.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.2, version: 0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,109 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,109 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,109 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,110 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,111 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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06:24:09,112 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-09-03 06:24:09,112 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (71.572 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,118 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,119 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,120 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,121 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,122 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,123 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,124 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,125 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,126 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,127 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,128 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,129 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,130 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,131 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,132 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,133 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,134 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,135 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,136 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,137 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,138 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,139 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,140 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,141 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,142 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,143 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,144 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,145 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,146 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,147 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,147 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,147 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,147 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,147 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,147 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,147 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,147 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,147 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,147 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,147 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,148 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,149 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,149 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,150 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,151 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,152 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,153 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,154 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,155 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,156 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,157 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,158 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,159 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,160 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,161 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,161 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,161 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,161 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,161 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,161 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,161 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,161 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,161 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,162 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,162 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,162 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,162 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,162 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,162 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,162 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,162 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,163 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,163 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,163 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,163 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,163 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,163 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,163 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,163 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,163 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,163 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,164 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,165 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,165 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,165 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,165 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, version: 1.7.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,165 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,165 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0, version: 0.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,166 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2, version: 1.6.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,166 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.4.3+galaxy10, version: 1.4.3+galaxy10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 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toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_open_reference/qiime2__vsearch__cluster_features_open_reference/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 2024-09-03 06:24:09,187 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__merge_pairs/qiime2__vsearch__merge_pairs/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 2024-09-03 06:24:09,187 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__uchime_denovo/qiime2__vsearch__uchime_denovo/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 2024-09-03 06:24:09,187 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__dereplicate_sequences/qiime2__vsearch__dereplicate_sequences/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 2024-09-03 06:24:09,187 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__fastq_stats/qiime2__vsearch__fastq_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 2024-09-03 06:24:09,187 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__uchime_ref/qiime2__vsearch__uchime_ref/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 2024-09-03 06:24:09,187 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_de_novo/qiime2__vsearch__cluster_features_de_novo/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 2024-09-03 06:24:09,188 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,188 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1, version: 1.0.8.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,188 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0, version: 1.0.11.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,188 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,188 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.2, version: 0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,188 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,188 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,189 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,189 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,189 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,189 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,189 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,189 [pN:job_handler_0,p:8,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 2024-09-03 06:24:09,189 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,189 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,190 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,191 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,192 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,192 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:24:09,192 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-09-03 06:24:09,192 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (79.548 ms) +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,193 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,194 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,195 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,196 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,197 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,198 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,199 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,200 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,201 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,202 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,203 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-09-03 06:24:09,206 [pN:job_handler_0,p:8,tN:Thread-1] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-09-03 06:24:09,212 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-09-03 06:24:09,214 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-09-03 06:24:09,218 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-09-03 06:24:09,219 [pN:job_handler_0,p:8,tN:Thread-1] Loaded data fetch tool: __DATA_FETCH__ +galaxy.queue_worker INFO 2024-09-03 06:24:09,219 [pN:job_handler_0,p:8,tN:Thread-1] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.queue_worker DEBUG 2024-09-03 06:24:09,223 [pN:job_handler_0,p:8,tN:Thread-1] Toolbox reload (328.931 ms) +galaxy.queue_worker INFO 2024-09-03 06:24:09,225 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker DEBUG 2024-09-03 06:24:09,225 [pN:job_handler_0,p:8,tN:Thread-1] App is not a webapp, not building a search index +galaxy.model.database_heartbeat DEBUG 2024-09-03 06:24:49,886 [pN:job_handler_0,p:8,tN:database_heartbeart_job_handler_0.thread] job_handler_0 is not config watcher +galaxy.jobs.handler DEBUG 2024-09-03 06:26:11,124 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 1 +tpv.rules.gateway INFO 2024-09-03 06:26:11,159 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] loading tpv rules from: ['https://raw.githubusercontent.com/galaxyproject/tpv-shared-database/main/tools.yml', 'lib/galaxy/jobs/rules/tpv_rules_local.yml', 'https://gist.githubusercontent.com/afgane/68d1dbbe0af2468ba347dc74b6d3f7fa/raw/20edda50161bdcb74ff38935e7f76d79bfdaf303/tvp_rules_tests.yml'] +tpv.rules.gateway INFO 2024-09-03 06:26:11,664 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Watching for changes in file: lib/galaxy/jobs/rules/tpv_rules_local.yml +tpv.core.entities DEBUG 2024-09-03 06:26:11,733 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:26:11,733 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:26:11,745 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:26:11,765 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:26:11,801 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Working directory for job is: /galaxy/server/database/jobs_directory/000/1 +galaxy.jobs.runners DEBUG 2024-09-03 06:26:11,814 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [1] queued (69.668 ms) +galaxy.jobs.handler INFO 2024-09-03 06:26:11,819 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (1) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:26:11,822 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 1 +galaxy.jobs DEBUG 2024-09-03 06:26:11,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [1] prepared (126.753 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:26:11,979 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/1/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/1/registry.xml' '/galaxy/server/database/jobs_directory/000/1/upload_params.json' '1:/galaxy/server/database/objects/0/b/a/dataset_0ba5d077-2fd3-4d97-8b5b-a34154168183_files:/galaxy/server/database/objects/0/b/a/dataset_0ba5d077-2fd3-4d97-8b5b-a34154168183.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:26:11,998 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (1) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/1/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/1/galaxy_1.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:26:12,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 1 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:26:12,031 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 1 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:26:12,531 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-09-03 06:26:12,823 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 2 +tpv.core.entities DEBUG 2024-09-03 06:26:12,852 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:26:12,852 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:26:12,857 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:26:12,868 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:26:12,883 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Working directory for job is: /galaxy/server/database/jobs_directory/000/2 +galaxy.jobs.runners DEBUG 2024-09-03 06:26:12,892 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [2] queued (35.470 ms) +galaxy.jobs.handler INFO 2024-09-03 06:26:12,894 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:26:12,897 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 2 +galaxy.jobs DEBUG 2024-09-03 06:26:12,968 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [2] prepared (64.131 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:26:12,984 [pN:job_handler_0,p:8,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/9/5/d/dataset_95da33ab-f618-4e90-9816-59b7efabc33c_files:/galaxy/server/database/objects/9/5/d/dataset_95da33ab-f618-4e90-9816-59b7efabc33c.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:26:12,991 [pN:job_handler_0,p:8,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.kubernetes DEBUG 2024-09-03 06:26:13,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 2 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:26:13,017 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 2 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:26:13,583 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.queue_worker INFO 2024-09-03 06:26:21,358 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'reload_toolbox' task, executing now. +galaxy.queue_worker DEBUG 2024-09-03 06:26:21,358 [pN:job_handler_0,p:8,tN:Thread-1] Executing toolbox reload on 'job_handler_0' +galaxy.util WARNING 2024-09-03 06:26:21,378 [pN:job_handler_0,p:8,tN:Thread-1] directory not found: /galaxy/server/config/plugins/activities +galaxy.tools WARNING 2024-09-03 06:26:21,384 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:26:21,384 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,384 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for tool configuration /galaxy/server/config/tool_conf.xml is None +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:26:21,385 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_importer.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:26:21,385 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'genomespace/genomespace_push.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:26:21,387 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/codingSnps.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:26:21,387 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool configuration file from path 'evolution/add_scores.xml': [Errno 2] No such file or directory +galaxy.tool_util.toolbox.base ERROR 2024-09-03 06:26:21,388 [pN:job_handler_0,p:8,tN:Thread-1] Error reading tool from path: phenotype_association/sift.xml +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 881, in _load_tool_tag_set + tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tool_util/toolbox/base.py", line 1108, in load_tool + tool = self.create_tool( + ^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 548, in create_tool + return self._create_tool_from_source(tool_source, config_file=config_file, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 564, in _create_tool_from_source + return create_tool_from_source(self.app, tool_source, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 356, in create_tool_from_source + tool = ToolClass(config_file, tool_source, app, **kwds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 821, in __init__ + raise e + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 818, in __init__ + self.parse(tool_source, guid=guid, dynamic=dynamic) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1143, in parse + self.parse_inputs(self.tool_source) + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1428, in parse_inputs + inputs = self.parse_input_elem(page_source, enctypes) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1623, in parse_input_elem + param = self.parse_param_elem(input_source, enctypes, context) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/__init__.py", line 1636, in parse_param_elem + param = ToolParameter.build(self, input_source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 335, in build + return parameter_types[param_type](tool, input_source) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 2078, in __init__ + super().__init__(tool, input_source, trans) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 1868, in __init__ + super().__init__(tool, input_source) + File "/galaxy/server/lib/galaxy/tools/parameters/basic.py", line 191, in __init__ + self.validators.append(validation.Validator.from_element(self, elem)) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 45, in from_element + return validator_types[_type].from_element(param, elem) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/galaxy/server/lib/galaxy/tools/parameters/validation.py", line 399, in from_element + assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found" + ^^^^^^^^^^^^^^^^^^^^^^^^ +AssertionError: File /galaxy/server/database/tool-data/sift_db.loc specified by the 'filename' attribute not found +galaxy.tools WARNING 2024-09-03 06:26:21,390 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:26:21,390 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,401 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /cvmfs/cloud.galaxyproject.org/config/shed_tool_conf.xml is /cvmfs/cloud.galaxyproject.org/tools +galaxy.tools WARNING 2024-09-03 06:26:21,428 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:26:21,428 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:26:21,428 [pN:job_handler_0,p:8,tN:Thread-1] Shed-enabled tool configuration file does not exist, but will be created on demand: /galaxy/server/config/mutable/editable_shed_tool_conf.xml +galaxy.tools WARNING 2024-09-03 06:26:21,428 [pN:job_handler_0,p:8,tN:Thread-1] The default shed tool config file (/galaxy/server/config/mutable/editable_shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file +galaxy.tool_util.toolbox.base INFO 2024-09-03 06:26:21,428 [pN:job_handler_0,p:8,tN:Thread-1] Parsing the tool configuration /galaxy/server/config/migrated_tools_conf.xml +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,428 [pN:job_handler_0,p:8,tN:Thread-1] Tool path for shed tool configuration /galaxy/server/config/migrated_tools_conf.xml is /galaxy/server/database/shed_tools +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,429 [pN:job_handler_0,p:8,tN:Thread-1] Reading tools from config files finished (44.841 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,429 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Get Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,429 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,429 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,429 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,429 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,429 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,429 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,430 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,431 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,431 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,431 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,431 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,431 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Send Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,431 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Expression Tools +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,431 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,431 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,431 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,431 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Collection Operations +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,431 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,431 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,431 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,431 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,432 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,433 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,434 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,435 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,436 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,437 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Filter and Sort +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,437 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded label: GFF +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,438 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Join, Subtract and Group +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,438 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Datamash +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,438 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,439 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTA/FASTQ +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,439 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,440 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,440 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: FASTQ Quality Control +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,441 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,442 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: SAM/BAM +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,442 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,443 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,444 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,445 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,446 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: BED +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,446 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,447 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,448 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,449 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,450 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: VCF/BCF +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,450 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,451 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,452 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,453 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,454 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,455 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Nanopore +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,456 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,457 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Convert Formats +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,457 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,458 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,458 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Lift-Over +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,458 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Virology +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,458 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,459 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Operate on Genomic Intervals +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,459 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Fetch Sequences/Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,459 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,460 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Assembly +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,460 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Annotation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,460 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mapping +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,460 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,461 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,461 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Variant Calling +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,462 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,463 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,463 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,463 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,463 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,463 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,463 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,463 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,463 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,463 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,463 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,463 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,463 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,464 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,464 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,464 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,464 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,464 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,464 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,464 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,464 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,464 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,464 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,464 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: ChIP-seq +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,465 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA-seq +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,465 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,465 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,465 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,465 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,465 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,465 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,465 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,465 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,465 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,465 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,466 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,466 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,466 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,466 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,466 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,466 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,466 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Multiple Alignments +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Phenotype Association +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,467 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Regional Variation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: STR-FM: Microsatellite Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Motif +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Chromosome Conformation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Mothur +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Picard +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,468 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,469 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,469 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,469 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,469 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,469 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,469 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,469 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,469 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,469 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,469 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,470 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,470 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,470 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,470 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,470 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,470 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,470 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,470 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,470 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,470 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,470 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,470 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,470 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,471 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Pharmacology +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,471 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,471 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Single-Cell +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,471 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,471 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,471 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,471 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,471 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,471 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,472 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,472 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,472 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,472 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,472 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,472 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,472 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,472 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,472 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,472 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,472 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,473 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,473 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,473 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,473 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,473 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,473 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,473 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,473 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,473 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,473 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,473 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,473 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,474 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__dereplicate_sequences/qiime2__vsearch__dereplicate_sequences/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 2024-09-03 06:26:21,498 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__fastq_stats/qiime2__vsearch__fastq_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 2024-09-03 06:26:21,498 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__uchime_ref/qiime2__vsearch__uchime_ref/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 2024-09-03 06:26:21,498 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,499 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RSeQC +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,499 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,499 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,499 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,499 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,500 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,500 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,500 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,500 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,500 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,500 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,500 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,500 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,500 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,500 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,500 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,500 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,501 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,501 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,501 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,501 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,501 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,501 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,501 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,501 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,501 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: MiModD +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,502 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Du Novo +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,502 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Seqtk +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,502 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: TRANSIT +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,502 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Statistics +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,502 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,502 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,502 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Graph/Display Data +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,502 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,502 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,503 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,503 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,503 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,503 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,503 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,503 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,503 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,504 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,504 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,504 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,504 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,504 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,504 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,504 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,504 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,504 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,505 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: RNA Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,505 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: CloudMap (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,505 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Metagenomic Analysis (deprecated) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,505 [pN:job_handler_0,p:8,tN:Thread-1] Loading section: Text Manipulation +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,505 [pN:job_handler_0,p:8,tN:Thread-1] Loading tool panel finished (76.148 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,510 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,511 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,512 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,513 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,514 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,515 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,516 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,517 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,518 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,519 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,520 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,520 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,520 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,520 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,520 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,520 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,520 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,520 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,520 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,520 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,520 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,520 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,521 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,521 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,521 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,521 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,521 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,521 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,521 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,521 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,521 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,521 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,521 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,521 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,521 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,522 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,522 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,522 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,522 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,522 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,522 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,522 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,522 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,522 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,523 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,524 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,524 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,524 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,524 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,524 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,524 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,524 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,524 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,524 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,525 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,525 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,525 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,525 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,525 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,525 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,525 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,525 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,525 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,526 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,526 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,526 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,526 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,526 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,526 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,526 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,526 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,526 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,526 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,526 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,526 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,527 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,527 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,527 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,527 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,527 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,527 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,527 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,527 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,527 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,527 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,527 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,528 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,528 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,528 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,528 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,528 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,528 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,528 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,528 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,528 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,528 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,529 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,529 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,529 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,529 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,529 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,529 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,529 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,529 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,529 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,529 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,529 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,530 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,530 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,530 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,530 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,530 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,530 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,530 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,530 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,530 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,530 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,530 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,530 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,531 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,531 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,531 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,531 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,531 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,531 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,531 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,531 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,532 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,532 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,532 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,532 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,532 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,532 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,532 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,532 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,533 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,533 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,533 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,533 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,533 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,533 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,533 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,534 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,534 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,534 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,534 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,534 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,534 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,534 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,534 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,534 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,534 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,535 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,535 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,535 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,535 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,535 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,535 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,535 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,535 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,535 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,535 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,535 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,535 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,535 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,536 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,537 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,538 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,539 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,540 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,541 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,542 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,543 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,544 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,545 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,546 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,547 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,548 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,549 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,550 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,551 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,552 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,553 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,553 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,553 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,553 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,553 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,553 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,553 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,553 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,553 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,553 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,553 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,554 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,554 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,554 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2, version: 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,554 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,554 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, version: 1.7.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,554 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,554 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0, version: 0.0.1+galaxy0 into tool panel.... 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version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,563 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,563 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,563 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,563 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__beta_group_significance/qiime2__diversity__beta_group_significance/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,563 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__procrustes_analysis/qiime2__diversity__procrustes_analysis/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,563 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity__mantel/qiime2__diversity__mantel/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,563 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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DEBUG 2024-09-03 06:26:21,566 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__blast/qiime2__feature_classifier__blast/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,566 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__find_consensus_annotation/qiime2__feature_classifier__find_consensus_annotation/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,566 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_classifier__vsearch_global/qiime2__feature_classifier__vsearch_global/2022.11.1+q2galaxy.2022.11.1.2, version: 2022.11.1+q2galaxy.2022.11.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0, version: 1.0.11.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.2, version: 0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,576 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,576 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,576 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,577 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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+galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,578 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,578 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,578 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,578 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,578 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: 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06:26:21,579 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-09-03 06:26:21,579 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (74.363 ms) +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,585 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0, version: 3.50.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2, version: 2.11.40.7+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0, version: 1.50.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1, version: 4.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, version: 0.4.8.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,586 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,587 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0, version: 1.16.11+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1, version: 1.16.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,588 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5, version: 0.0.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,589 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,589 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a, version: 2.7.8a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,589 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1, version: 2.7.8a+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,589 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, version: 1.10.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,589 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0, version: 1.8+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,589 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Summary_Statistics1, version: 1.1.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,589 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5, version: 1.1.5 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0, version: 1.2.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1, version: 1.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3, version: 1.0+galaxy3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,590 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_stacked/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy7, version: 0.69.8+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0, version: 2.10.9+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0, version: 0.2.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1, version: 2.11.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,591 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0, version: 2.11.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: upload1, version: 1.1.7 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: intermine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: flymine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mousemine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ratmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wormbase, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,592 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hbvar, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: export_remote, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1, version: 0.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: param_value_from_file, version: 0.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0, version: 0.5.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0, version: 5.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_EMPTY_DATASETS__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,593 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __TAG_FROM_FILE__, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __APPLY_RULES__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __BUILD_LIST__, version: 1.1.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: __EXTRACT_DATASET__, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, version: 3.7+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.2, version: 3.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6, version: 1.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0, version: 3.12.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,594 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1, version: 1.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2, version: 0.9.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4, version: 0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0, version: 0.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,595 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0, version: 0.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1, version: 1.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2, version: 1.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2, version: 1.4.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0, version: 1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2, version: 1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,596 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1, version: 0.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2, version: 0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: addValue, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: cat1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: createInterval, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Cut1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Paste1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: random_lines1, version: 2.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show beginning1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Show tail1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: trimmer, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,597 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: secure_hash_message_digest, version: 0.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, version: 3.3.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1, version: 3.14.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0, version: 2.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0, version: 1.2.4+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4, version: 1.1.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1, version: 0.1.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0+galaxy0, version: 1.1.0+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,598 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1, version: 3.16.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Filter1, version: 1.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: sort1, version: 1.2.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grep1, version: 1.0.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: join1, version: 2.1.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: comp1, version: 1.0.2 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,599 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Grouping1, version: 2.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2, version: 1.1.0+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.8, version: 1.16.8 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4, version: 1.2.11.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3, version: 0.6.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1, version: 0.5.5.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,600 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2, version: 1.1.2+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7, version: 0.2.7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2, version: 0.1.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0, version: 0.20.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1, version: 0.72+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, version: 0.38.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,601 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0, version: 1.11+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0, version: 0.73+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1, version: 1.11+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0, version: 0.23.2+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,602 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3, version: 1.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3, version: 2.2.2d+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3, version: 1.9+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1+galaxy1, version: 2.0.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, version: 1.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0, version: 2.4.0.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamtools_split/2.4.0, version: 2.4.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_multi_bamqc/qualimap_multi_bamqc/2.2.2d, version: 2.2.2d into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.9+galaxy2, version: 1.9+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,603 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1, version: 1.9+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2, version: 2.0.2+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.9, version: 1.9 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2, version: 2.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1, version: 1.8+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4, version: 2.1.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,604 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1, version: 2.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1, version: 2.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2, version: 1.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0, version: 1.2.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.2, version: 2.0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4, version: 2.0.4 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,605 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1, version: 2.5.2+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0, version: 1.15.1+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2, version: 0.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,606 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,607 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.2, version: 2.30.0.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,608 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0, version: 2.30.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2, version: 2.30.0+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3, version: 2.30.0.3 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,609 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy1, version: 2.30.0+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,610 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_gtcheck/bcftools_gtcheck/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fixploidy/bcftools_plugin_fixploidy/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_missing2ref/bcftools_plugin_missing2ref/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts/bcftools_plugin_counts/1.10+galaxy1, version: 1.10+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,611 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_reheader/bcftools_reheader/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_tags/bcftools_plugin_fill_tags/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_view/bcftools_view/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_filter/bcftools_filter/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage/bcftools_plugin_dosage/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,612 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_tag2tag/bcftools_plugin_tag2tag/1.10, version: 1.10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,613 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0, version: 1.0.0_rc3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3, version: 1.0.0_rc3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/vcfdistance/vcfdistance/1.0.0_rc1+galaxy0, version: 1.0.0_rc1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,614 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.0.3+galaxy7, version: 1.0.3+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6, version: 2.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant_pipeline/medaka_variant_pipeline/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus/medaka_consensus/1.0.3+galaxy2, version: 1.0.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1, version: 1.28.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,615 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.1, version: 0.6.1a1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, version: 0.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_times/poretools_times/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0, version: 0.6.1a1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,616 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: wig_to_bigWig, version: 1.1.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: bed_to_bigBed, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: liftOver1, version: 1.0.6 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.2.2+galaxy1, version: 1.2.2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19, version: 4.5covid19 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_filtervariants/ivar_filtervariants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0, version: 1.2.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: wiggle2simple1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,617 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Extract genomic DNA 1, version: 2.2.4 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,618 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1, version: 3.12.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0, version: 0.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13, version: 1.4.13 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4, version: 2.17+galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0, version: 2.4.2+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4, version: 0.7.17.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1, version: 0.7.17.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2, version: 0.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2, version: 1.3.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2, version: 2.5.2b-2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,619 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5, version: 0.7.17.5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2, version: 0.7.17.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1, version: 2.1.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0, version: 2.1.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1, version: 1.3.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_genesets/snpSift_geneSets/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0, version: 4.3.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,620 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4, version: 4.3+T.galaxy4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1, version: 4.3+T.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_caseControl/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1, version: 4.3+t.galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0, version: 4.3+t.galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0, version: 1.0.12+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,621 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/jasminesv/jasminesv/1.0.11+galaxy1, version: 1.0.11+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2, version: 2.1.5+galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, version: 1.3.6+galaxy0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6, version: 1.3.6 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy5, version: 4.3+T.galaxy5 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2, version: 4.3+T.galaxy2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,622 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1, version: 4.3r.1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1, version: 1.3.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1, version: 0.46.0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4, version: 0.46.0.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1, version: 2.11.40.6+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3, version: 3.38.3+galaxy3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1, version: 3.24.1+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1, version: 0.10.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7, version: 2.1.0+galaxy7 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1, version: 2.1.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2, version: 2.0.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, version: 2.2.1+galaxy1 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,623 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3, version: 2.2.1.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0, version: 1.1.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0, version: 1.20.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1, version: 1.8.0+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1, version: 4.0.0beta2+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,624 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_david, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,625 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3, version: 2.18.2.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,626 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_artifact_metrics/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.2, version: 2.18.2.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,627 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectHsMetrics/2.18.2, version: 2.18.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1, version: 2.18.2.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0, version: 1.3.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/10x_bamtofastq/10x_bamtofastq/1.4.1, version: 1.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,628 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a, version: 1.5.a into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy0, version: 0.7.5+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1, version: 0.7.5+galaxy1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0, version: 1.0.4+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,629 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy2, version: 0.2.3+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/salmonquantmerge/salmonquantmerge/1.5.1+galaxy0, version: 1.5.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/imgteam/slice_image/ip_slice_image/0.3, version: 0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_normalize/scater_normalize/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2, version: 1.12.2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.22.0, version: 1.22.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,630 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... 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[pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0, version: 1.7.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0, version: 0.0.1+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2, version: 1.6.1+galaxy2 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,631 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.4.3+galaxy10, version: 1.4.3+galaxy10 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 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toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__barplot/qiime2__taxa__barplot/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 2024-09-03 06:26:21,652 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__taxa__filter_seqs/qiime2__taxa__filter_seqs/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 2024-09-03 06:26:21,652 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_closed_reference/qiime2__vsearch__cluster_features_closed_reference/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 2024-09-03 06:26:21,652 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_open_reference/qiime2__vsearch__cluster_features_open_reference/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 2024-09-03 06:26:21,652 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__merge_pairs/qiime2__vsearch__merge_pairs/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 2024-09-03 06:26:21,652 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__uchime_denovo/qiime2__vsearch__uchime_denovo/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 2024-09-03 06:26:21,652 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__dereplicate_sequences/qiime2__vsearch__dereplicate_sequences/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 2024-09-03 06:26:21,652 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__fastq_stats/qiime2__vsearch__fastq_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 2024-09-03 06:26:21,652 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__uchime_ref/qiime2__vsearch__uchime_ref/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 2024-09-03 06:26:21,653 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__vsearch__cluster_features_de_novo/qiime2__vsearch__cluster_features_de_novo/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 2024-09-03 06:26:21,653 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,653 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1, version: 1.0.8.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,653 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0, version: 1.0.11.0 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,653 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,653 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.2, version: 0.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,653 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0, version: 1.0.11.0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,654 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1, version: 0.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,654 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,654 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,654 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,654 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,654 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,654 [pN:job_handler_0,p:8,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 2024-09-03 06:26:21,655 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_deletion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,655 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,655 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,655 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,655 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,655 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,656 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,656 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_mismatch_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,656 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,656 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,656 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_hexamer/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,656 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_insertion_profile/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,657 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,657 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,657 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_GC/2.6.4, version: 2.6.4 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,657 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1, version: 2.6.4.1 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,657 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,657 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.2, version: 2.6.4.2 into tool panel. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,657 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: Count1, version: 1.0.3 into tool panel.. +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,658 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6, version: 3.6 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,658 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3, version: 0.0.3 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,658 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0, version: 1.34.0+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,658 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0, version: 3.1.3+galaxy0 into tool panel.... +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,658 [pN:job_handler_0,p:8,tN:Thread-1] Skipping tool panel addition of hidden tool: qual_stats_boxplot, version: 1.0.1 +galaxy.tool_util.toolbox.base DEBUG 2024-09-03 06:26:21,658 [pN:job_handler_0,p:8,tN:Thread-1] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel.. +galaxy.tool_util.toolbox.views.edam DEBUG 2024-09-03 06:26:21,658 [pN:job_handler_0,p:8,tN:Thread-1] Loading EDAM tool panel finished (78.793 ms) +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,659 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,659 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,659 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,659 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,659 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,659 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,659 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,659 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,659 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,660 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,660 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,660 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,660 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cram_to_bam_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,660 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,660 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,660 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,660 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,660 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,660 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,660 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,660 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_parquet_to_csv +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: bigwigtowig +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: csv_to_tabular +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fasta_to_fai +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,661 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,662 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,662 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,662 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,662 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,662 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,662 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,662 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,662 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,662 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,662 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,662 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,663 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,663 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,663 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,663 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,663 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,663 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,663 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,663 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,663 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,663 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,663 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,663 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,663 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bz2_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,664 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,665 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_tar_to_directory +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,665 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,665 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,665 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,665 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,665 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,665 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,665 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,665 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,665 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,665 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,665 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,665 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,665 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,666 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,666 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,666 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_unsorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,666 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,666 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bam_to_qname_sorted_bam +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,666 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,666 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,666 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: tabular_to_csv +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,666 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,667 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_uncompressed_to_gz +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_gz_to_uncompressed +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_biom +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_SMILES_to_MOL +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_smiles_to_smiles +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,668 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_inchi_to_mol +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mol2_to_mol +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_cml_to_smiles +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,669 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_molecules +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Pdb_to_Gro_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_mdconvert +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_Gro_to_Pdb_0 +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_ref_to_seq_taxomony +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,670 [pN:job_handler_0,p:8,tN:Thread-1] Loaded converter: CONVERTER_neostorezip_to_neostore +galaxy.datatypes.registry DEBUG 2024-09-03 06:26:21,671 [pN:job_handler_0,p:8,tN:Thread-1] Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2024-09-03 06:26:21,672 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export tool: __EXPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-09-03 06:26:21,673 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history export to uri tool: __EXPORT_HISTORY_TO_URI__ +galaxy.tools.special_tools DEBUG 2024-09-03 06:26:21,674 [pN:job_handler_0,p:8,tN:Thread-1] Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2024-09-03 06:26:21,675 [pN:job_handler_0,p:8,tN:Thread-1] Loaded data fetch tool: __DATA_FETCH__ +galaxy.queue_worker INFO 2024-09-03 06:26:21,675 [pN:job_handler_0,p:8,tN:Thread-1] Queuing async task rebuild_toolbox_search_index for job_handler_0. +galaxy.queue_worker DEBUG 2024-09-03 06:26:21,676 [pN:job_handler_0,p:8,tN:Thread-1] Toolbox reload (318.375 ms) +galaxy.queue_worker INFO 2024-09-03 06:26:21,677 [pN:job_handler_0,p:8,tN:Thread-1] Instance 'job_handler_0' received 'rebuild_toolbox_search_index' task, executing now. +galaxy.queue_worker DEBUG 2024-09-03 06:26:21,677 [pN:job_handler_0,p:8,tN:Thread-1] App is not a webapp, not building a search index +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:26:35,171 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ntr99 with k8s id: gxy-ntr99 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:26:35,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-z8lhp with k8s id: gxy-z8lhp succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:26:35,337 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 1: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:26:35,355 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 2: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:26:42,705 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 1 finished +galaxy.model.metadata DEBUG 2024-09-03 06:26:42,751 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 1 +galaxy.jobs INFO 2024-09-03 06:26:42,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 1 in /galaxy/server/database/jobs_directory/000/1 +galaxy.jobs.runners DEBUG 2024-09-03 06:26:42,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 2 finished +galaxy.jobs DEBUG 2024-09-03 06:26:42,866 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 1 executed (139.200 ms) +galaxy.model.metadata DEBUG 2024-09-03 06:26:42,878 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 2 +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:26:42,879 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 1 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs INFO 2024-09-03 06:26:42,919 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 2 in /galaxy/server/database/jobs_directory/000/2 +galaxy.jobs DEBUG 2024-09-03 06:26:42,970 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 2 executed (118.076 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:26:42,983 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 2 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:26:43,453 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 3 +tpv.core.entities DEBUG 2024-09-03 06:26:43,489 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/miniasm/miniasm/.*, abstract=False, cores=1, mem=32, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:26:43,490 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:26:43,492 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:26:43,501 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:26:43,516 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Working directory for job is: /galaxy/server/database/jobs_directory/000/3 +galaxy.jobs.runners DEBUG 2024-09-03 06:26:43,525 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [3] queued (32.289 ms) +galaxy.jobs.handler INFO 2024-09-03 06:26:43,527 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (3) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:26:43,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 3 +galaxy.jobs DEBUG 2024-09-03 06:26:43,585 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [3] prepared (46.901 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:26:43,585 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:26:43,585 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0: miniasm:0.3 +galaxy.tool_util.deps.mulled.util DEBUG 2024-09-03 06:26:43,588 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Querying https://quay.io/api/v1/repository for repos within biocontainers +galaxy.tool_util.deps.containers INFO 2024-09-03 06:27:06,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/miniasm:0.3--he4a0461_3,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:27:06,871 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/3/tool_script.sh] for tool command [miniasm -V > /galaxy/server/database/jobs_directory/000/3/outputs/COMMAND_VERSION 2>&1; +miniasm -f '/galaxy/server/database/objects/0/b/a/dataset_0ba5d077-2fd3-4d97-8b5b-a34154168183.dat' -m '100' -i '0.05' -s '1000' -c '3' -o '1000' -h '1000' -I '0.08' -g '1000' -d '50000' -e '4' -n '3' -F '0.8' '/galaxy/server/database/objects/9/5/d/dataset_95da33ab-f618-4e90-9816-59b7efabc33c.dat' > '/galaxy/server/database/objects/1/1/0/dataset_11078dd4-bda0-4ef4-b2d9-afcf16426295.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:27:06,894 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (3) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/3/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/3/galaxy_3.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:06,913 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 3 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:27:06,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:27:06,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0: miniasm:0.3 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:27:06,941 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/miniasm:0.3--he4a0461_3,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:06,969 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 3 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:07,301 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:13,398 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-xfwpj with k8s id: gxy-xfwpj succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:27:13,538 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 3: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:27:20,608 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 3 finished +galaxy.model.metadata DEBUG 2024-09-03 06:27:20,648 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 3 +galaxy.jobs INFO 2024-09-03 06:27:20,689 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 3 in /galaxy/server/database/jobs_directory/000/3 +galaxy.jobs DEBUG 2024-09-03 06:27:20,729 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 3 executed (101.044 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:20,741 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 3 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:27:22,139 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 4 +tpv.core.entities DEBUG 2024-09-03 06:27:22,164 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:27:22,165 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:27:22,168 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:27:22,178 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:27:22,193 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Working directory for job is: /galaxy/server/database/jobs_directory/000/4 +galaxy.jobs.runners DEBUG 2024-09-03 06:27:22,199 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [4] queued (31.148 ms) +galaxy.jobs.handler INFO 2024-09-03 06:27:22,202 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (4) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:22,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 4 +galaxy.jobs DEBUG 2024-09-03 06:27:22,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [4] prepared (69.710 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:27:22,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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/9/7/b/dataset_97b02566-59f7-453e-b759-3f75fa0eab19_files:/galaxy/server/database/objects/9/7/b/dataset_97b02566-59f7-453e-b759-3f75fa0eab19.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:27:22,309 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (4) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/4/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/4/galaxy_4.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:22,320 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 4 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:22,333 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 4 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:22,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-09-03 06:27:23,206 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 5 +tpv.core.entities DEBUG 2024-09-03 06:27:23,224 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:27:23,225 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:27:23,228 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:27:23,239 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:27:23,253 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Working directory for job is: /galaxy/server/database/jobs_directory/000/5 +galaxy.jobs.runners DEBUG 2024-09-03 06:27:23,259 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [5] queued (31.378 ms) +galaxy.jobs.handler INFO 2024-09-03 06:27:23,261 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:23,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 5 +galaxy.jobs DEBUG 2024-09-03 06:27:23,339 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [5] prepared (68.661 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:27:23,359 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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/4/4/5/dataset_445026e0-dc80-4d1c-95a7-ef2a720e4cfe_files:/galaxy/server/database/objects/4/4/5/dataset_445026e0-dc80-4d1c-95a7-ef2a720e4cfe.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:27:23,368 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:23,380 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 5 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:23,392 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 5 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:23,521 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:32,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-shsh9 with k8s id: gxy-shsh9 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:27:32,866 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 4: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.kubernetes DEBUG 2024-09-03 06:27:33,742 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ds469 with k8s id: gxy-ds469 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:27:33,890 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 5: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:27:40,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 4 finished +galaxy.model.metadata DEBUG 2024-09-03 06:27:40,359 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 4 +galaxy.jobs INFO 2024-09-03 06:27:40,393 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 4 in /galaxy/server/database/jobs_directory/000/4 +galaxy.jobs DEBUG 2024-09-03 06:27:40,439 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 4 executed (100.671 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:40,450 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 4 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-09-03 06:27:41,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 5 finished +galaxy.model.metadata DEBUG 2024-09-03 06:27:41,453 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 5 +galaxy.jobs INFO 2024-09-03 06:27:41,486 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 5 in /galaxy/server/database/jobs_directory/000/5 +galaxy.jobs DEBUG 2024-09-03 06:27:41,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 5 executed (100.276 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:41,542 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 5 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:27:41,853 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 6 +tpv.core.entities DEBUG 2024-09-03 06:27:41,881 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/miniasm/miniasm/.*, abstract=False, cores=1, mem=32, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:27:41,882 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:27:41,886 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:27:41,897 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:27:41,911 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Working directory for job is: /galaxy/server/database/jobs_directory/000/6 +galaxy.jobs.runners DEBUG 2024-09-03 06:27:41,919 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [6] queued (33.793 ms) +galaxy.jobs.handler INFO 2024-09-03 06:27:41,922 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:41,924 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 6 +galaxy.jobs DEBUG 2024-09-03 06:27:41,974 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [6] prepared (41.954 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:27:41,975 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:27:41,975 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0: miniasm:0.3 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:27:41,997 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/miniasm:0.3--he4a0461_3,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:27:42,021 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/6/tool_script.sh] for tool command [miniasm -V > /galaxy/server/database/jobs_directory/000/6/outputs/COMMAND_VERSION 2>&1; +miniasm -f '/galaxy/server/database/objects/9/7/b/dataset_97b02566-59f7-453e-b759-3f75fa0eab19.dat' -m '99' -i '0.04' -s '999' -c '2' -o '999' -h '999' -I '0.7' -g '999' -d '45000' -e '3' -n '2' -F '0.7' '/galaxy/server/database/objects/4/4/5/dataset_445026e0-dc80-4d1c-95a7-ef2a720e4cfe.dat' > '/galaxy/server/database/objects/6/8/7/dataset_68788490-b501-4324-aad6-a96ec5989fb7.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:27:42,040 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:42,059 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 6 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:27:42,065 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:27:42,065 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0: miniasm:0.3 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:27:42,084 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/miniasm:0.3--he4a0461_3,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:42,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 6 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:42,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:45,838 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-vrzpp with k8s id: gxy-vrzpp succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:27:45,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 6: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:27:52,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 6 finished +galaxy.model.metadata DEBUG 2024-09-03 06:27:52,914 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 6 +galaxy.jobs INFO 2024-09-03 06:27:52,998 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 6 in /galaxy/server/database/jobs_directory/000/6 +galaxy.jobs DEBUG 2024-09-03 06:27:53,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 6 executed (151.912 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:53,067 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 6 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:27:55,146 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 7 +tpv.core.entities DEBUG 2024-09-03 06:27:55,172 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:27:55,172 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:27:55,176 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:27:55,186 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:27:55,199 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Working directory for job is: /galaxy/server/database/jobs_directory/000/7 +galaxy.jobs.runners DEBUG 2024-09-03 06:27:55,207 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [7] queued (30.588 ms) +galaxy.jobs.handler INFO 2024-09-03 06:27:55,209 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:55,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 7 +galaxy.jobs DEBUG 2024-09-03 06:27:55,293 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [7] prepared (73.170 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:27:55,315 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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/e/0/3/dataset_e039fab3-2355-42f1-9d32-5425785170fc_files:/galaxy/server/database/objects/e/0/3/dataset_e039fab3-2355-42f1-9d32-5425785170fc.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:27:55,324 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (7) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/7/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/7/galaxy_7.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:55,339 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 7 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:55,353 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 7 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:27:55,863 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:28:04,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-z6bhw with k8s id: gxy-z6bhw succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:28:05,116 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 7: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:28:12,121 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 7 finished +galaxy.model.metadata DEBUG 2024-09-03 06:28:12,163 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 7 +galaxy.jobs INFO 2024-09-03 06:28:12,196 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 7 in /galaxy/server/database/jobs_directory/000/7 +galaxy.jobs DEBUG 2024-09-03 06:28:12,254 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 7 executed (114.811 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:28:12,267 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 7 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:28:12,474 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 8 +tpv.core.entities DEBUG 2024-09-03 06:28:12,501 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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_bigwig_compare/deeptools_bigwig_compare/.*, abstract=False, cores=10, mem=24, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:28:12,502 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:28:12,506 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:28:12,518 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:28:12,531 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Working directory for job is: /galaxy/server/database/jobs_directory/000/8 +galaxy.jobs.runners DEBUG 2024-09-03 06:28:12,540 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [8] queued (33.466 ms) +galaxy.jobs.handler INFO 2024-09-03 06:28:12,542 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:28:12,544 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 8 +galaxy.jobs DEBUG 2024-09-03 06:28:12,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [8] prepared (47.163 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:28:12,601 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:28:12,601 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-09-03 06:28:12,779 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:28:12,801 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/8/tool_script.sh] for tool command [bigwigCompare --version > /galaxy/server/database/jobs_directory/000/8/outputs/COMMAND_VERSION 2>&1; +bigwigCompare --numberOfProcessors "${GALAXY_SLOTS:-4}" --bigwig1 '/galaxy/server/database/objects/e/0/3/dataset_e039fab3-2355-42f1-9d32-5425785170fc.dat' --bigwig2 '/galaxy/server/database/objects/e/0/3/dataset_e039fab3-2355-42f1-9d32-5425785170fc.dat' --outFileName '/galaxy/server/database/objects/4/5/2/dataset_452bce42-c8cf-4492-8c7e-2e1b3986b61e.dat' --outFileFormat 'bigwig' --operation ratio --pseudocount 1 1] +galaxy.jobs.runners DEBUG 2024-09-03 06:28:12,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (8) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/8/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/8/galaxy_8.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:28:12,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 8 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:28:12,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:28:12,844 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-09-03 06:28:12,862 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:28:12,881 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 8 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:28:13,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:28:39,347 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-dxs8h with k8s id: gxy-dxs8h succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:28:39,477 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 8: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:28:46,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 8 finished +galaxy.model.metadata DEBUG 2024-09-03 06:28:46,668 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 8 +galaxy.util WARNING 2024-09-03 06:28:46,673 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/4/5/2/dataset_452bce42-c8cf-4492-8c7e-2e1b3986b61e.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/4/5/2/dataset_452bce42-c8cf-4492-8c7e-2e1b3986b61e.dat' +galaxy.jobs INFO 2024-09-03 06:28:46,699 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 8 in /galaxy/server/database/jobs_directory/000/8 +galaxy.jobs DEBUG 2024-09-03 06:28:46,749 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 8 executed (105.221 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:28:46,762 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 8 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:28:48,116 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 9 +tpv.core.entities DEBUG 2024-09-03 06:28:48,139 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:28:48,140 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:28:48,144 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:28:48,155 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:28:48,169 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Working directory for job is: /galaxy/server/database/jobs_directory/000/9 +galaxy.jobs.runners DEBUG 2024-09-03 06:28:48,175 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [9] queued (31.628 ms) +galaxy.jobs.handler INFO 2024-09-03 06:28:48,178 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:28:48,180 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 9 +galaxy.jobs DEBUG 2024-09-03 06:28:48,257 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [9] prepared (70.313 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:28:48,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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/f/4/8/dataset_f483d3e6-616c-40d5-9371-41ebf0051e41_files:/galaxy/server/database/objects/f/4/8/dataset_f483d3e6-616c-40d5-9371-41ebf0051e41.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:28:48,287 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (9) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/9/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/9/galaxy_9.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:28:48,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 9 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:28:48,312 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 9 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:28:49,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:28:57,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-s8fgk with k8s id: gxy-s8fgk succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:28:57,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 9: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:29:04,494 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 9 finished +galaxy.model.metadata DEBUG 2024-09-03 06:29:04,531 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 9 +galaxy.jobs INFO 2024-09-03 06:29:04,560 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 9 in /galaxy/server/database/jobs_directory/000/9 +galaxy.jobs DEBUG 2024-09-03 06:29:04,608 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 9 executed (96.034 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:04,620 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 9 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:29:05,451 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 10 +tpv.core.entities DEBUG 2024-09-03 06:29:05,475 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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_bigwig_compare/deeptools_bigwig_compare/.*, abstract=False, cores=10, mem=24, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:29:05,475 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:29:05,478 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:29:05,486 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:29:05,500 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Working directory for job is: /galaxy/server/database/jobs_directory/000/10 +galaxy.jobs.runners DEBUG 2024-09-03 06:29:05,509 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [10] queued (30.809 ms) +galaxy.jobs.handler INFO 2024-09-03 06:29:05,511 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:05,514 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 10 +galaxy.jobs DEBUG 2024-09-03 06:29:05,557 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [10] prepared (36.267 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:29:05,557 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:29:05,557 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-09-03 06:29:05,577 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:29:05,597 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/10/tool_script.sh] for tool command [bigwigCompare --version > /galaxy/server/database/jobs_directory/000/10/outputs/COMMAND_VERSION 2>&1; +bigwigCompare --numberOfProcessors "${GALAXY_SLOTS:-4}" --bigwig1 '/galaxy/server/database/objects/f/4/8/dataset_f483d3e6-616c-40d5-9371-41ebf0051e41.dat' --bigwig2 '/galaxy/server/database/objects/f/4/8/dataset_f483d3e6-616c-40d5-9371-41ebf0051e41.dat' --outFileName '/galaxy/server/database/objects/2/b/5/dataset_2b5710c7-2215-4b4b-b62f-f5ee29b55ee5.dat' --outFileFormat 'bedgraph' --operation ratio --pseudocount 1 1] +galaxy.jobs.runners DEBUG 2024-09-03 06:29:05,609 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (10) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/10/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/10/galaxy_10.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:05,629 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 10 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:29:05,636 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:29:05,636 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c +galaxy.tool_util.deps.containers INFO 2024-09-03 06:29:05,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:336148be6fa4ca2fe5a75db2297a83862c17e65c-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:05,687 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 10 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:06,523 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:10,603 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-xpfkf with k8s id: gxy-xpfkf succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:29:10,722 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 10: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:29:17,770 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 10 finished +galaxy.model.metadata DEBUG 2024-09-03 06:29:17,817 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 10 +galaxy.util WARNING 2024-09-03 06:29:17,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/2/b/5/dataset_2b5710c7-2215-4b4b-b62f-f5ee29b55ee5.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/b/5/dataset_2b5710c7-2215-4b4b-b62f-f5ee29b55ee5.dat' +galaxy.jobs INFO 2024-09-03 06:29:17,849 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 10 in /galaxy/server/database/jobs_directory/000/10 +galaxy.jobs DEBUG 2024-09-03 06:29:17,888 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 10 executed (97.093 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:17,901 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 10 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:29:19,748 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 11 +tpv.core.entities DEBUG 2024-09-03 06:29:19,768 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:29:19,768 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:29:19,771 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:29:19,779 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:29:19,793 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Working directory for job is: /galaxy/server/database/jobs_directory/000/11 +galaxy.jobs.runners DEBUG 2024-09-03 06:29:19,799 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [11] queued (28.099 ms) +galaxy.jobs.handler INFO 2024-09-03 06:29:19,801 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:19,804 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 11 +galaxy.jobs DEBUG 2024-09-03 06:29:19,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [11] prepared (66.460 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:29:19,894 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/11/tool_script.sh] for tool command [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/8/4/a/dataset_84afcfcf-bac3-49e0-ab39-bc8799f549a2_files:/galaxy/server/database/objects/8/4/a/dataset_84afcfcf-bac3-49e0-ab39-bc8799f549a2.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:29:19,903 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (11) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/11/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/11/galaxy_11.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:19,915 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 11 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:19,928 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 11 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:20,626 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:29,875 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-pzjtn with k8s id: gxy-pzjtn succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:29:29,994 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 11: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:29:36,996 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 11 finished +galaxy.model.metadata DEBUG 2024-09-03 06:29:37,036 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 11 +galaxy.jobs INFO 2024-09-03 06:29:37,070 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 11 in /galaxy/server/database/jobs_directory/000/11 +galaxy.jobs DEBUG 2024-09-03 06:29:37,120 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 11 executed (105.836 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:37,133 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 11 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:29:38,079 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 12 +tpv.core.entities DEBUG 2024-09-03 06:29:38,106 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:29:38,106 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:29:38,110 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:29:38,120 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:29:38,137 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Working directory for job is: /galaxy/server/database/jobs_directory/000/12 +galaxy.jobs.runners DEBUG 2024-09-03 06:29:38,147 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [12] queued (36.643 ms) +galaxy.jobs.handler INFO 2024-09-03 06:29:38,149 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:38,152 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 12 +galaxy.jobs DEBUG 2024-09-03 06:29:38,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [12] prepared (42.752 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:29:38,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:29:38,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:29:38,385 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:29:38,408 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/12/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/8/4/a/dataset_84afcfcf-bac3-49e0-ab39-bc8799f549a2.dat' sanger '/galaxy/server/database/objects/4/5/f/dataset_45fc0db9-f527-4765-914b-5e67126b160c.dat' sanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2024-09-03 06:29:38,422 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (12) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/12/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/12/galaxy_12.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:38,436 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 12 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:29:38,443 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:29:38,443 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:29:38,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:38,478 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 12 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:38,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:48,014 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-x5m54 with k8s id: gxy-x5m54 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:29:48,127 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 12: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:29:54,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 12 finished +galaxy.model.metadata DEBUG 2024-09-03 06:29:55,016 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 12 +galaxy.jobs INFO 2024-09-03 06:29:55,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 12 in /galaxy/server/database/jobs_directory/000/12 +galaxy.jobs DEBUG 2024-09-03 06:29:55,086 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 12 executed (91.783 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:55,098 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 12 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:29:56,432 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 13 +tpv.core.entities DEBUG 2024-09-03 06:29:56,451 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:29:56,452 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:29:56,455 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:29:56,464 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:29:56,475 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Working directory for job is: /galaxy/server/database/jobs_directory/000/13 +galaxy.jobs.runners DEBUG 2024-09-03 06:29:56,481 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [13] queued (25.680 ms) +galaxy.jobs.handler INFO 2024-09-03 06:29:56,483 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:56,485 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 13 +galaxy.jobs DEBUG 2024-09-03 06:29:56,557 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [13] prepared (63.197 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:29:56,579 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/13/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/13/registry.xml' '/galaxy/server/database/jobs_directory/000/13/upload_params.json' '13:/galaxy/server/database/objects/5/a/a/dataset_5aa7c81e-febe-4b9c-ab8e-c7a1dc0e881f_files:/galaxy/server/database/objects/5/a/a/dataset_5aa7c81e-febe-4b9c-ab8e-c7a1dc0e881f.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:29:56,590 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (13) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/13/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/13/galaxy_13.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:56,606 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 13 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:56,621 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 13 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:29:57,040 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:06,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-wqqjf with k8s id: gxy-wqqjf succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:30:06,319 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 13: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:30:13,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 13 finished +galaxy.model.metadata DEBUG 2024-09-03 06:30:13,460 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 13 +galaxy.jobs INFO 2024-09-03 06:30:13,490 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 13 in /galaxy/server/database/jobs_directory/000/13 +galaxy.jobs DEBUG 2024-09-03 06:30:13,539 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 13 executed (101.865 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:13,551 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 13 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:30:14,773 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 14 +tpv.core.entities DEBUG 2024-09-03 06:30:14,800 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:30:14,801 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:30:14,804 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:30:14,814 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:30:14,826 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Working directory for job is: /galaxy/server/database/jobs_directory/000/14 +galaxy.jobs.runners DEBUG 2024-09-03 06:30:14,833 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [14] queued (28.787 ms) +galaxy.jobs.handler INFO 2024-09-03 06:30:14,835 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:14,837 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 14 +galaxy.jobs DEBUG 2024-09-03 06:30:14,881 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [14] prepared (36.136 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:30:14,882 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:30:14,882 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:30:14,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:30:14,919 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/14/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/5/a/a/dataset_5aa7c81e-febe-4b9c-ab8e-c7a1dc0e881f.dat' sanger '/galaxy/server/database/objects/1/a/e/dataset_1ae19e53-0a24-4fa6-8727-04b08eed2e69.dat' sanger ascii summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:30:14,928 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:14,941 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 14 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:30:14,941 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:30:14,942 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:30:14,959 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:14,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 14 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:15,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:19,285 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-7x2pc with k8s id: gxy-7x2pc succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:30:19,414 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 14: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:30:26,290 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 14 finished +galaxy.model.metadata DEBUG 2024-09-03 06:30:26,327 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 14 +galaxy.jobs INFO 2024-09-03 06:30:26,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 14 in /galaxy/server/database/jobs_directory/000/14 +galaxy.jobs DEBUG 2024-09-03 06:30:26,398 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 14 executed (89.736 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:26,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 14 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:30:28,166 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 15 +tpv.core.entities DEBUG 2024-09-03 06:30:28,190 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:30:28,190 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:30:28,194 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:30:28,204 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:30:28,217 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Working directory for job is: /galaxy/server/database/jobs_directory/000/15 +galaxy.jobs.runners DEBUG 2024-09-03 06:30:28,225 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [15] queued (30.342 ms) +galaxy.jobs.handler INFO 2024-09-03 06:30:28,227 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:28,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 15 +galaxy.jobs DEBUG 2024-09-03 06:30:28,315 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [15] prepared (77.373 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:30:28,335 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/3/4/4/dataset_3443d596-7865-4b06-a918-b42375674ca6_files:/galaxy/server/database/objects/3/4/4/dataset_3443d596-7865-4b06-a918-b42375674ca6.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:30:28,345 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:28,360 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 15 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:28,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 15 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:29,308 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:38,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-pct86 with k8s id: gxy-pct86 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:30:38,537 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 15: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:30:45,442 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 15 finished +galaxy.model.metadata DEBUG 2024-09-03 06:30:45,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 15 +galaxy.jobs INFO 2024-09-03 06:30:45,527 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 15 in /galaxy/server/database/jobs_directory/000/15 +galaxy.jobs DEBUG 2024-09-03 06:30:45,573 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 15 executed (110.279 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:45,585 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 15 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:30:46,502 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 16 +tpv.core.entities DEBUG 2024-09-03 06:30:46,524 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:30:46,524 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:30:46,527 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:30:46,536 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:30:46,548 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Working directory for job is: /galaxy/server/database/jobs_directory/000/16 +galaxy.jobs.runners DEBUG 2024-09-03 06:30:46,555 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [16] queued (28.453 ms) +galaxy.jobs.handler INFO 2024-09-03 06:30:46,557 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:46,559 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 16 +galaxy.jobs DEBUG 2024-09-03 06:30:46,610 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [16] prepared (43.446 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:30:46,610 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:30:46,611 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:30:46,634 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:30:46,655 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/16/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/3/4/4/dataset_3443d596-7865-4b06-a918-b42375674ca6.dat' sanger '/galaxy/server/database/objects/f/d/3/dataset_fd35fc07-8dea-4bb5-b485-7bf007537abc.dat' sanger ascii summarize_input --no-fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:30:46,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (16) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/16/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/16/galaxy_16.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:46,683 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 16 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:30:46,689 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:30:46,690 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:30:46,711 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:46,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 16 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:47,447 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:51,510 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-wqm8m failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:51,511 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:51,527 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job: gxy-wqm8m failed due to an unknown exit code from the tool. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:51,531 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 16 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-09-03 06:30:51,689 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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 2024-09-03 06:30:58,717 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 16 finished +galaxy.tool_util.output_checker INFO 2024-09-03 06:30:58,729 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job failed because of contents in the standard error stream: [Traceback (most recent call last): + File "/usr/local/bin/gx-fastq-groomer", line 10, in + sys.exit(main()) + ^^^^^^ + File "/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py", line 99, in main + Groomer().run() + File "/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py", line 48, in run + for read_count, fastq_read in enumerate(reader): + File "/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py", line 683, in __iter__ + yield next(self) + ^^^^^^^^^^ + File "/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py", line 742, in __next__ + raise e + File "/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py", line 724, in __next__ + block = super(fastqVerboseErrorReader, self).__next__() + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py", line 621, in __next__ + self._read_fastq_sequence(rval, id_line) + File "/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py", line 666, in _read_fastq_sequence + raise fastqFormatError( +galaxy_utils.sequence.fastq.fastqFormatError: Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1). +] +galaxy.jobs DEBUG 2024-09-03 06:30:58,785 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (16) setting dataset 16 state to ERROR +galaxy.jobs INFO 2024-09-03 06:30:58,806 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 16 in /galaxy/server/database/jobs_directory/000/16 +galaxy.jobs DEBUG 2024-09-03 06:30:58,846 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 16 executed (108.746 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:58,857 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 16 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:30:59,765 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 17 +tpv.core.entities DEBUG 2024-09-03 06:30:59,790 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:30:59,790 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:30:59,793 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:30:59,804 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:30:59,818 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Working directory for job is: /galaxy/server/database/jobs_directory/000/17 +galaxy.jobs.runners DEBUG 2024-09-03 06:30:59,825 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [17] queued (31.562 ms) +galaxy.jobs.handler INFO 2024-09-03 06:30:59,827 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:59,829 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 17 +galaxy.jobs DEBUG 2024-09-03 06:30:59,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [17] prepared (80.228 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:30:59,935 [pN:job_handler_0,p:8,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/9/4/f/dataset_94fee34c-4103-4f79-9dba-cfe66412a7e1_files:/galaxy/server/database/objects/9/4/f/dataset_94fee34c-4103-4f79-9dba-cfe66412a7e1.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:30:59,945 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:59,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 17 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:30:59,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 17 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:00,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:09,916 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-r24l9 with k8s id: gxy-r24l9 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:31:10,038 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 17: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:31:16,990 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 17 finished +galaxy.model.metadata DEBUG 2024-09-03 06:31:17,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 17 +galaxy.jobs INFO 2024-09-03 06:31:17,061 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 17 in /galaxy/server/database/jobs_directory/000/17 +galaxy.jobs DEBUG 2024-09-03 06:31:17,117 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 17 executed (106.770 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:17,129 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 17 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:31:18,112 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 18 +tpv.core.entities DEBUG 2024-09-03 06:31:18,136 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:31:18,137 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:31:18,140 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:31:18,149 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:31:18,162 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Working directory for job is: /galaxy/server/database/jobs_directory/000/18 +galaxy.jobs.runners DEBUG 2024-09-03 06:31:18,170 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [18] queued (29.684 ms) +galaxy.jobs.handler INFO 2024-09-03 06:31:18,172 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:18,174 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 18 +galaxy.jobs DEBUG 2024-09-03 06:31:18,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [18] prepared (41.093 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:31:18,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:31:18,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:31:18,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:31:18,264 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/18/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/9/4/f/dataset_94fee34c-4103-4f79-9dba-cfe66412a7e1.dat' sanger '/galaxy/server/database/objects/4/d/1/dataset_4d10b5a3-867a-4461-8959-3ba23cee6a17.dat' sanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2024-09-03 06:31:18,279 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (18) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/18/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/18/galaxy_18.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:18,295 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 18 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:31:18,303 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:31:18,304 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:31:18,321 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:18,341 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 18 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:18,940 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:23,083 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-cskwz failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:23,084 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:23,134 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-cskwz. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:23,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 18 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-09-03 06:31:23,198 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-09-03-06-11-1/jobs/gxy-cskwz + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-cskwz": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:23,206 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:23,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (18/gxy-cskwz) tool_stdout: Groomed 2 sanger reads into sanger reads. +Based upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2 +Input ASCII range: '!'(33) - '~'(126) +Input decimal range: 0 - 93 + +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:23,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (18/gxy-cskwz) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:23,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (18/gxy-cskwz) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:23,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (18/gxy-cskwz) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-cskwz. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:23,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Attempting to stop job 18 (gxy-cskwz) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:23,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Found job with id gxy-cskwz to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:23,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 18 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:23,291 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (18/gxy-cskwz) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-09-03 06:31:24,252 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 19 +tpv.core.entities DEBUG 2024-09-03 06:31:24,277 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:31:24,277 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:31:24,280 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:31:24,290 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:31:24,304 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Working directory for job is: /galaxy/server/database/jobs_directory/000/19 +galaxy.jobs.runners DEBUG 2024-09-03 06:31:24,312 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [19] queued (31.774 ms) +galaxy.jobs.handler INFO 2024-09-03 06:31:24,315 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:24,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 19 +galaxy.jobs DEBUG 2024-09-03 06:31:24,388 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [19] prepared (63.929 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:31:24,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/2/a/e/dataset_2ae28f22-d864-4303-9934-3b3cf77d7af1_files:/galaxy/server/database/objects/2/a/e/dataset_2ae28f22-d864-4303-9934-3b3cf77d7af1.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:31:24,414 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:24,424 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 19 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:24,436 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 19 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:25,223 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:33,338 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-5mnbz with k8s id: gxy-5mnbz succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:31:33,455 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 19: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.runners DEBUG 2024-09-03 06:31:40,457 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 19 finished +galaxy.model.metadata DEBUG 2024-09-03 06:31:40,500 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 19 +galaxy.jobs INFO 2024-09-03 06:31:40,529 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 19 in /galaxy/server/database/jobs_directory/000/19 +galaxy.jobs DEBUG 2024-09-03 06:31:40,576 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 19 executed (98.876 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:40,589 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 19 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:31:41,571 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 20 +tpv.core.entities DEBUG 2024-09-03 06:31:41,598 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:31:41,598 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:31:41,601 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:31:41,612 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:31:41,625 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Working directory for job is: /galaxy/server/database/jobs_directory/000/20 +galaxy.jobs.runners DEBUG 2024-09-03 06:31:41,635 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [20] queued (33.491 ms) +galaxy.jobs.handler INFO 2024-09-03 06:31:41,637 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:41,639 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 20 +galaxy.jobs DEBUG 2024-09-03 06:31:41,689 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [20] prepared (41.978 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:31:41,690 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:31:41,690 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:31:41,711 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:31:41,730 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/20/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/2/a/e/dataset_2ae28f22-d864-4303-9934-3b3cf77d7af1.dat' cssanger '/galaxy/server/database/objects/3/d/d/dataset_3dd0903b-f73a-478d-bcee-94ec7b9a6004.dat' cssanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2024-09-03 06:31:41,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (20) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/20/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/20/galaxy_20.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:41,757 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 20 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:31:41,765 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:31:41,765 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:31:41,785 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:41,806 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 20 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:42,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:46,421 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-vsn67 with k8s id: gxy-vsn67 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:31:46,539 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 20: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:31:53,504 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 20 finished +galaxy.model.metadata DEBUG 2024-09-03 06:31:53,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 20 +galaxy.jobs INFO 2024-09-03 06:31:53,576 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 20 in /galaxy/server/database/jobs_directory/000/20 +galaxy.jobs DEBUG 2024-09-03 06:31:53,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 20 executed (93.551 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:53,629 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 20 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:31:54,852 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 21 +tpv.core.entities DEBUG 2024-09-03 06:31:54,875 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:31:54,875 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:31:54,878 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:31:54,886 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:31:54,898 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Working directory for job is: /galaxy/server/database/jobs_directory/000/21 +galaxy.jobs.runners DEBUG 2024-09-03 06:31:54,905 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [21] queued (27.019 ms) +galaxy.jobs.handler INFO 2024-09-03 06:31:54,908 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:54,910 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 21 +galaxy.jobs DEBUG 2024-09-03 06:31:54,983 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [21] prepared (67.224 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:31:55,002 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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/6/b/1/dataset_6b1e972f-a41e-46ef-8dcd-6aaffc7e7e51_files:/galaxy/server/database/objects/6/b/1/dataset_6b1e972f-a41e-46ef-8dcd-6aaffc7e7e51.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:31:55,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (21) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/21/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/21/galaxy_21.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:55,023 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 21 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:55,036 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 21 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:31:55,444 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:04,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-z5dlm with k8s id: gxy-z5dlm succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:32:04,678 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 21: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:32:11,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 21 finished +galaxy.model.metadata DEBUG 2024-09-03 06:32:11,774 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 21 +galaxy.jobs INFO 2024-09-03 06:32:11,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 21 in /galaxy/server/database/jobs_directory/000/21 +galaxy.jobs DEBUG 2024-09-03 06:32:11,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 21 executed (104.424 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:11,866 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 21 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:32:12,191 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 22 +tpv.core.entities DEBUG 2024-09-03 06:32:12,221 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:32:12,222 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:32:12,225 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:32:12,238 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:32:12,254 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Working directory for job is: /galaxy/server/database/jobs_directory/000/22 +galaxy.jobs.runners DEBUG 2024-09-03 06:32:12,263 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [22] queued (37.210 ms) +galaxy.jobs.handler INFO 2024-09-03 06:32:12,265 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:12,268 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 22 +galaxy.jobs DEBUG 2024-09-03 06:32:12,327 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [22] prepared (47.261 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:32:12,327 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:32:12,327 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:32:12,518 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:32:12,542 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/22/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/6/b/1/dataset_6b1e972f-a41e-46ef-8dcd-6aaffc7e7e51.dat' illumina '/galaxy/server/database/objects/a/6/f/dataset_a6f1559e-fec2-4f88-a11e-9e46bb62a69d.dat' sanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2024-09-03 06:32:12,557 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:12,577 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 22 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:32:12,587 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:32:12,587 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:32:12,609 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:12,633 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 22 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:13,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:17,646 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-2962d with k8s id: gxy-2962d succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:32:17,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 22: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:32:24,695 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 22 finished +galaxy.model.metadata DEBUG 2024-09-03 06:32:24,730 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 22 +galaxy.jobs INFO 2024-09-03 06:32:24,756 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 22 in /galaxy/server/database/jobs_directory/000/22 +galaxy.jobs DEBUG 2024-09-03 06:32:24,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 22 executed (82.186 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:24,804 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 22 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:32:25,559 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 23 +tpv.core.entities DEBUG 2024-09-03 06:32:25,585 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:32:25,586 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:32:25,588 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:32:25,599 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:32:25,615 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Working directory for job is: /galaxy/server/database/jobs_directory/000/23 +galaxy.jobs.runners DEBUG 2024-09-03 06:32:25,622 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [23] queued (33.659 ms) +galaxy.jobs.handler INFO 2024-09-03 06:32:25,625 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:25,627 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 23 +galaxy.jobs DEBUG 2024-09-03 06:32:25,717 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [23] prepared (83.453 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:32:25,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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/a/8/0/dataset_a80cdb30-ddfb-46c7-ab25-c6dadb54ea8c_files:/galaxy/server/database/objects/a/8/0/dataset_a80cdb30-ddfb-46c7-ab25-c6dadb54ea8c.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:32:25,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (23) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/23/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/23/galaxy_23.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:25,782 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 23 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:25,795 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 23 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:26,670 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:35,796 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-78fwk with k8s id: gxy-78fwk succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:32:35,914 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 23: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.jobs.runners DEBUG 2024-09-03 06:32:42,882 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 23 finished +galaxy.model.metadata DEBUG 2024-09-03 06:32:42,934 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 23 +galaxy.jobs INFO 2024-09-03 06:32:42,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 23 in /galaxy/server/database/jobs_directory/000/23 +galaxy.jobs DEBUG 2024-09-03 06:32:43,010 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 23 executed (98.075 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:43,022 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 23 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:32:43,911 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 24 +tpv.core.entities DEBUG 2024-09-03 06:32:43,937 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:32:43,938 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:32:43,941 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:32:43,952 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:32:43,969 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Working directory for job is: /galaxy/server/database/jobs_directory/000/24 +galaxy.jobs.runners DEBUG 2024-09-03 06:32:43,978 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [24] queued (37.349 ms) +galaxy.jobs.handler INFO 2024-09-03 06:32:43,980 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:43,983 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 24 +galaxy.jobs DEBUG 2024-09-03 06:32:44,028 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [24] prepared (39.330 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:32:44,029 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:32:44,029 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:32:44,048 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:32:44,069 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/24/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/a/8/0/dataset_a80cdb30-ddfb-46c7-ab25-c6dadb54ea8c.dat' solexa '/galaxy/server/database/objects/5/1/c/dataset_51c059e8-550b-407b-a59c-c17d8b5acf87.dat' sanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2024-09-03 06:32:44,081 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:44,099 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 24 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:32:44,107 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:32:44,107 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:32:44,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:44,147 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 24 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:44,838 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:48,900 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-rsmtj with k8s id: gxy-rsmtj succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:32:49,023 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 24: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:32:56,149 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 24 finished +galaxy.model.metadata DEBUG 2024-09-03 06:32:56,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 24 +galaxy.jobs INFO 2024-09-03 06:32:56,241 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 24 in /galaxy/server/database/jobs_directory/000/24 +galaxy.jobs DEBUG 2024-09-03 06:32:56,288 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 24 executed (116.700 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:56,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 24 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:32:57,202 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 25 +tpv.core.entities DEBUG 2024-09-03 06:32:57,232 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:32:57,232 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:32:57,237 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:32:57,250 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:32:57,267 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Working directory for job is: /galaxy/server/database/jobs_directory/000/25 +galaxy.jobs.runners DEBUG 2024-09-03 06:32:57,274 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [25] queued (37.449 ms) +galaxy.jobs.handler INFO 2024-09-03 06:32:57,277 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:57,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 25 +galaxy.jobs DEBUG 2024-09-03 06:32:57,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [25] prepared (69.743 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:32:57,379 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/25/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/25/registry.xml' '/galaxy/server/database/jobs_directory/000/25/upload_params.json' '25:/galaxy/server/database/objects/6/2/c/dataset_62ca17a8-eff0-4d23-bbcd-5bc03aa86779_files:/galaxy/server/database/objects/6/2/c/dataset_62ca17a8-eff0-4d23-bbcd-5bc03aa86779.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:32:57,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (25) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/25/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/25/galaxy_25.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:57,402 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 25 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:57,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 25 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:32:57,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:07,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-xgxzw with k8s id: gxy-xgxzw succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:33:07,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 25: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:33:14,329 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 25 finished +galaxy.model.metadata DEBUG 2024-09-03 06:33:14,370 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 25 +galaxy.jobs INFO 2024-09-03 06:33:14,402 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 25 in /galaxy/server/database/jobs_directory/000/25 +galaxy.jobs DEBUG 2024-09-03 06:33:14,452 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 25 executed (103.524 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:14,464 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 25 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:33:15,566 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 26 +tpv.core.entities DEBUG 2024-09-03 06:33:15,591 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:33:15,592 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:33:15,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:33:15,609 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:33:15,624 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Working directory for job is: /galaxy/server/database/jobs_directory/000/26 +galaxy.jobs.runners DEBUG 2024-09-03 06:33:15,631 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [26] queued (35.610 ms) +galaxy.jobs.handler INFO 2024-09-03 06:33:15,634 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:15,635 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 26 +galaxy.jobs DEBUG 2024-09-03 06:33:15,696 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [26] prepared (53.732 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:33:15,696 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:33:15,696 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:33:15,717 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:33:15,737 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/26/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/6/2/c/dataset_62ca17a8-eff0-4d23-bbcd-5bc03aa86779.dat' sanger '/galaxy/server/database/objects/2/b/4/dataset_2b4e232a-f34a-40a5-9950-ba0c67ef33ba.dat' sanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2024-09-03 06:33:15,770 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:15,787 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 26 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:33:15,794 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:33:15,794 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:33:15,812 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:15,832 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 26 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:16,158 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:20,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-pvrtl with k8s id: gxy-pvrtl succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:33:20,342 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 26: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:33:27,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 26 finished +galaxy.model.metadata DEBUG 2024-09-03 06:33:27,399 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 26 +galaxy.jobs INFO 2024-09-03 06:33:27,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 26 in /galaxy/server/database/jobs_directory/000/26 +galaxy.jobs DEBUG 2024-09-03 06:33:27,470 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 26 executed (91.770 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:27,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 26 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:33:28,832 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 27 +tpv.core.entities DEBUG 2024-09-03 06:33:28,855 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:33:28,856 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:33:28,860 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:33:28,869 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:33:28,883 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Working directory for job is: /galaxy/server/database/jobs_directory/000/27 +galaxy.jobs.runners DEBUG 2024-09-03 06:33:28,889 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [27] queued (29.116 ms) +galaxy.jobs.handler INFO 2024-09-03 06:33:28,891 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:28,894 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 27 +galaxy.jobs DEBUG 2024-09-03 06:33:28,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [27] prepared (69.976 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:33:28,992 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/27/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/27/registry.xml' '/galaxy/server/database/jobs_directory/000/27/upload_params.json' '27:/galaxy/server/database/objects/4/1/1/dataset_411a4551-1b99-4adf-bc5b-3ba6a52a525b_files:/galaxy/server/database/objects/4/1/1/dataset_411a4551-1b99-4adf-bc5b-3ba6a52a525b.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:33:28,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (27) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/27/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/27/galaxy_27.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:29,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 27 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:29,025 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 27 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:29,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:38,388 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-8gxkk failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:38,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:38,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-8gxkk. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:38,428 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 27 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-09-03 06:33:38,478 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-09-03-06-11-1/jobs/gxy-8gxkk + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-8gxkk": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:38,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:38,495 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (27/gxy-8gxkk) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:38,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (27/gxy-8gxkk) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:38,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (27/gxy-8gxkk) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:38,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (27/gxy-8gxkk) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-8gxkk. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:38,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Attempting to stop job 27 (gxy-8gxkk) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:38,503 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Found job with id gxy-8gxkk to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:38,504 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 27 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:38,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (27/gxy-8gxkk) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-09-03 06:33:40,051 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 28 +tpv.core.entities DEBUG 2024-09-03 06:33:40,075 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:33:40,075 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:33:40,078 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:33:40,089 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:33:40,103 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Working directory for job is: /galaxy/server/database/jobs_directory/000/28 +galaxy.jobs.runners DEBUG 2024-09-03 06:33:40,111 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [28] queued (32.768 ms) +galaxy.jobs.handler INFO 2024-09-03 06:33:40,113 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:40,115 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 28 +galaxy.jobs DEBUG 2024-09-03 06:33:40,201 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [28] prepared (75.971 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:33:40,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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/a/f/6/dataset_af6ad6c0-fd93-4118-91cc-36452e80f696_files:/galaxy/server/database/objects/a/f/6/dataset_af6ad6c0-fd93-4118-91cc-36452e80f696.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:33:40,227 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (28) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/28/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/28/galaxy_28.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:40,241 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 28 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:40,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 28 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:40,520 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:49,647 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-cf4jd with k8s id: gxy-cf4jd succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:33:49,760 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 28: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:33:56,883 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 28 finished +galaxy.model.metadata DEBUG 2024-09-03 06:33:56,925 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 28 +galaxy.jobs INFO 2024-09-03 06:33:56,955 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 28 in /galaxy/server/database/jobs_directory/000/28 +galaxy.jobs DEBUG 2024-09-03 06:33:57,001 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 28 executed (97.297 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:57,014 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 28 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:33:57,556 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 29 +tpv.core.entities DEBUG 2024-09-03 06:33:57,582 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:33:57,582 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:33:57,585 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:33:57,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:33:57,608 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Working directory for job is: /galaxy/server/database/jobs_directory/000/29 +galaxy.jobs.runners DEBUG 2024-09-03 06:33:57,616 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [29] queued (30.722 ms) +galaxy.jobs.handler INFO 2024-09-03 06:33:57,619 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:57,621 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 29 +galaxy.jobs DEBUG 2024-09-03 06:33:57,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [29] prepared (33.534 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:33:57,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:33:57,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:33:57,681 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:33:57,701 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/29/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/a/f/6/dataset_af6ad6c0-fd93-4118-91cc-36452e80f696.dat' illumina '/galaxy/server/database/objects/4/1/a/dataset_41a6ab6d-a3b9-4fb6-a7c1-ebe1d3c3bfcd.dat' sanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:33:57,711 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (29) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/29/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/29/galaxy_29.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:57,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 29 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:33:57,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:33:57,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:33:57,753 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:57,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 29 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:33:58,675 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:01,720 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-rl95n with k8s id: gxy-rl95n succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:34:01,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 29: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:34:08,923 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 29 finished +galaxy.model.metadata DEBUG 2024-09-03 06:34:08,966 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 29 +galaxy.jobs INFO 2024-09-03 06:34:08,993 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 29 in /galaxy/server/database/jobs_directory/000/29 +galaxy.jobs DEBUG 2024-09-03 06:34:09,038 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 29 executed (95.103 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:09,050 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 29 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:34:10,847 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 30 +tpv.core.entities DEBUG 2024-09-03 06:34:10,872 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:34:10,873 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:34:10,876 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:34:10,885 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:34:10,898 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Working directory for job is: /galaxy/server/database/jobs_directory/000/30 +galaxy.jobs.runners DEBUG 2024-09-03 06:34:10,904 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [30] queued (28.271 ms) +galaxy.jobs.handler INFO 2024-09-03 06:34:10,907 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:10,908 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 30 +galaxy.jobs DEBUG 2024-09-03 06:34:10,988 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [30] prepared (72.332 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:34:11,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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/c/d/a/dataset_cda81f93-b68e-4544-9410-77d041445107_files:/galaxy/server/database/objects/c/d/a/dataset_cda81f93-b68e-4544-9410-77d041445107.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:34:11,018 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (30) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/30/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/30/galaxy_30.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:11,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 30 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:11,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 30 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:11,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:20,874 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-8rfhf with k8s id: gxy-8rfhf succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:34:20,997 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 30: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:34:28,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 30 finished +galaxy.model.metadata DEBUG 2024-09-03 06:34:28,088 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 30 +galaxy.jobs INFO 2024-09-03 06:34:28,120 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 30 in /galaxy/server/database/jobs_directory/000/30 +galaxy.jobs DEBUG 2024-09-03 06:34:28,167 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 30 executed (103.926 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:28,179 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 30 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:34:29,203 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 31 +tpv.core.entities DEBUG 2024-09-03 06:34:29,226 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:34:29,226 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:34:29,229 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:34:29,238 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:34:29,250 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Working directory for job is: /galaxy/server/database/jobs_directory/000/31 +galaxy.jobs.runners DEBUG 2024-09-03 06:34:29,258 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [31] queued (29.007 ms) +galaxy.jobs.handler INFO 2024-09-03 06:34:29,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:29,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 31 +galaxy.jobs DEBUG 2024-09-03 06:34:29,310 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [31] prepared (39.964 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:34:29,310 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:34:29,310 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:34:29,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:34:29,349 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/31/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/c/d/a/dataset_cda81f93-b68e-4544-9410-77d041445107.dat' illumina '/galaxy/server/database/objects/8/8/3/dataset_883e7139-af7c-4c37-b5f9-266d8bc5ec8a.dat' solexa None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:34:29,359 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:29,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 31 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:34:29,384 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:34:29,384 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:34:29,400 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:29,419 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 31 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:29,899 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:33,957 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-zvg7p with k8s id: gxy-zvg7p succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:34:34,075 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 31: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:34:41,155 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 31 finished +galaxy.model.metadata DEBUG 2024-09-03 06:34:41,201 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 31 +galaxy.jobs INFO 2024-09-03 06:34:41,231 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 31 in /galaxy/server/database/jobs_directory/000/31 +galaxy.jobs DEBUG 2024-09-03 06:34:41,270 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 31 executed (93.602 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:41,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 31 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:34:42,474 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 32 +tpv.core.entities DEBUG 2024-09-03 06:34:42,498 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:34:42,499 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:34:42,503 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:34:42,514 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:34:42,528 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Working directory for job is: /galaxy/server/database/jobs_directory/000/32 +galaxy.jobs.runners DEBUG 2024-09-03 06:34:42,534 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [32] queued (30.537 ms) +galaxy.jobs.handler INFO 2024-09-03 06:34:42,536 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:42,538 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 32 +galaxy.jobs DEBUG 2024-09-03 06:34:42,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [32] prepared (70.035 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:34:42,635 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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/4/b/dataset_d4bad188-0037-4979-b54a-2f338b860a02_files:/galaxy/server/database/objects/d/4/b/dataset_d4bad188-0037-4979-b54a-2f338b860a02.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:34:42,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (32) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/32/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/32/galaxy_32.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:42,656 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 32 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:42,670 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 32 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:42,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:52,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-m89hq with k8s id: gxy-m89hq succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:34:52,256 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 32: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:34:59,324 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 32 finished +galaxy.model.metadata DEBUG 2024-09-03 06:34:59,361 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 32 +galaxy.jobs INFO 2024-09-03 06:34:59,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 32 in /galaxy/server/database/jobs_directory/000/32 +galaxy.jobs DEBUG 2024-09-03 06:34:59,432 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 32 executed (89.576 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:59,443 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 32 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:34:59,836 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 33 +tpv.core.entities DEBUG 2024-09-03 06:34:59,863 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:34:59,863 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:34:59,867 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:34:59,878 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:34:59,891 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Working directory for job is: /galaxy/server/database/jobs_directory/000/33 +galaxy.jobs.runners DEBUG 2024-09-03 06:34:59,898 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [33] queued (30.896 ms) +galaxy.jobs.handler INFO 2024-09-03 06:34:59,900 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:34:59,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 33 +galaxy.jobs DEBUG 2024-09-03 06:34:59,951 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [33] prepared (41.021 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:34:59,951 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:34:59,952 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:34:59,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:34:59,992 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/33/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/d/4/b/dataset_d4bad188-0037-4979-b54a-2f338b860a02.dat' illumina '/galaxy/server/database/objects/5/4/b/dataset_54b12869-d0d6-4832-9ee6-5576678c477d.dat' cssanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:35:00,006 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:00,024 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 33 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:35:00,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:35:00,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:35:00,052 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:00,072 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 33 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:00,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:05,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-mfhnc with k8s id: gxy-mfhnc succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:35:05,438 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 33: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-03 06:35:12,553 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 33 finished +galaxy.model.metadata DEBUG 2024-09-03 06:35:12,597 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 33 +galaxy.jobs INFO 2024-09-03 06:35:12,631 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 33 in /galaxy/server/database/jobs_directory/000/33 +galaxy.jobs DEBUG 2024-09-03 06:35:12,683 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 33 executed (108.810 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:12,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 33 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:35:14,121 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 34 +tpv.core.entities DEBUG 2024-09-03 06:35:14,145 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:35:14,146 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:35:14,149 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:35:14,162 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:35:14,178 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Working directory for job is: /galaxy/server/database/jobs_directory/000/34 +galaxy.jobs.runners DEBUG 2024-09-03 06:35:14,187 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [34] queued (38.021 ms) +galaxy.jobs.handler INFO 2024-09-03 06:35:14,190 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:14,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 34 +galaxy.jobs DEBUG 2024-09-03 06:35:14,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [34] prepared (79.862 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:35:14,303 [pN:job_handler_0,p:8,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/8/8/2/dataset_8820800b-259e-4482-b5ee-0b8347cc68c3_files:/galaxy/server/database/objects/8/8/2/dataset_8820800b-259e-4482-b5ee-0b8347cc68c3.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:35:14,314 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:14,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 34 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:14,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 34 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:15,327 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:24,443 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-r2x6g with k8s id: gxy-r2x6g succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:35:24,557 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 34: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:35:31,523 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 34 finished +galaxy.model.metadata DEBUG 2024-09-03 06:35:31,564 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 34 +galaxy.jobs INFO 2024-09-03 06:35:31,596 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 34 in /galaxy/server/database/jobs_directory/000/34 +galaxy.jobs DEBUG 2024-09-03 06:35:31,641 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 34 executed (97.065 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:31,652 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 34 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:35:32,482 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 35 +tpv.core.entities DEBUG 2024-09-03 06:35:32,506 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:35:32,507 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:35:32,510 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:35:32,519 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:35:32,531 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Working directory for job is: /galaxy/server/database/jobs_directory/000/35 +galaxy.jobs.runners DEBUG 2024-09-03 06:35:32,538 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [35] queued (27.847 ms) +galaxy.jobs.handler INFO 2024-09-03 06:35:32,540 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:32,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 35 +galaxy.jobs DEBUG 2024-09-03 06:35:32,589 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [35] prepared (38.966 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:35:32,590 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:35:32,590 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:35:32,613 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:35:32,632 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/35/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/8/8/2/dataset_8820800b-259e-4482-b5ee-0b8347cc68c3.dat' sanger '/galaxy/server/database/objects/5/e/6/dataset_5e6118f6-b2c7-45e5-9dfa-ebd7761c9f1a.dat' sanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:35:32,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:32,659 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 35 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:35:32,667 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:35:32,667 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:35:32,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:32,708 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 35 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:33,468 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:37,536 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-sdfh9 with k8s id: gxy-sdfh9 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:35:37,669 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 35: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:35:44,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 35 finished +galaxy.model.metadata DEBUG 2024-09-03 06:35:44,588 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 35 +galaxy.jobs INFO 2024-09-03 06:35:44,624 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 35 in /galaxy/server/database/jobs_directory/000/35 +galaxy.jobs DEBUG 2024-09-03 06:35:44,667 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 35 executed (103.881 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:44,681 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 35 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:35:45,750 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 36 +tpv.core.entities DEBUG 2024-09-03 06:35:45,775 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:35:45,775 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:35:45,779 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:35:45,790 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:35:45,803 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Working directory for job is: /galaxy/server/database/jobs_directory/000/36 +galaxy.jobs.runners DEBUG 2024-09-03 06:35:45,809 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [36] queued (30.449 ms) +galaxy.jobs.handler INFO 2024-09-03 06:35:45,812 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:45,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 36 +galaxy.jobs DEBUG 2024-09-03 06:35:45,880 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [36] prepared (59.760 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:35:45,896 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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/f/0/3/dataset_f03aa1e7-e59d-4625-960e-1c9887c0c480_files:/galaxy/server/database/objects/f/0/3/dataset_f03aa1e7-e59d-4625-960e-1c9887c0c480.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:35:45,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (36) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/36/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/36/galaxy_36.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:45,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 36 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:45,929 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 36 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:46,560 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:35:54,677 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-db25t with k8s id: gxy-db25t succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:35:54,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 36: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:36:01,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 36 finished +galaxy.model.metadata DEBUG 2024-09-03 06:36:01,840 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 36 +galaxy.jobs INFO 2024-09-03 06:36:01,872 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 36 in /galaxy/server/database/jobs_directory/000/36 +galaxy.jobs DEBUG 2024-09-03 06:36:01,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 36 executed (99.076 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:01,928 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 36 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:36:02,079 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 37 +tpv.core.entities DEBUG 2024-09-03 06:36:02,103 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:36:02,104 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:36:02,107 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:36:02,117 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:36:02,131 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Working directory for job is: /galaxy/server/database/jobs_directory/000/37 +galaxy.jobs.runners DEBUG 2024-09-03 06:36:02,139 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [37] queued (31.648 ms) +galaxy.jobs.handler INFO 2024-09-03 06:36:02,141 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:02,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 37 +galaxy.jobs DEBUG 2024-09-03 06:36:02,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [37] prepared (42.682 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:36:02,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:36:02,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:36:02,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:36:02,236 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/37/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/f/0/3/dataset_f03aa1e7-e59d-4625-960e-1c9887c0c480.dat' sanger '/galaxy/server/database/objects/1/3/e/dataset_13ed8fbb-33a0-452d-8265-c9ebf6441412.dat' illumina None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:36:02,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (37) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/37/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/37/galaxy_37.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:02,267 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 37 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:36:02,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:36:02,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:36:02,295 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:02,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 37 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:02,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:06,763 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-8h5r7 with k8s id: gxy-8h5r7 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:36:06,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 37: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:36:13,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 37 finished +galaxy.model.metadata DEBUG 2024-09-03 06:36:13,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 37 +galaxy.jobs INFO 2024-09-03 06:36:13,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 37 in /galaxy/server/database/jobs_directory/000/37 +galaxy.jobs DEBUG 2024-09-03 06:36:14,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 37 executed (91.294 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:14,017 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 37 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:36:15,356 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 38 +tpv.core.entities DEBUG 2024-09-03 06:36:15,380 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:36:15,380 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:36:15,384 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:36:15,395 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:36:15,410 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Working directory for job is: /galaxy/server/database/jobs_directory/000/38 +galaxy.jobs.runners DEBUG 2024-09-03 06:36:15,416 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [38] queued (31.962 ms) +galaxy.jobs.handler INFO 2024-09-03 06:36:15,418 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:15,421 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 38 +galaxy.jobs DEBUG 2024-09-03 06:36:15,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [38] prepared (69.145 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:36:15,515 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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/f/9/7/dataset_f97a283f-f08f-4151-8f21-45982b5a59e8_files:/galaxy/server/database/objects/f/9/7/dataset_f97a283f-f08f-4151-8f21-45982b5a59e8.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:36:15,523 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (38) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/38/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/38/galaxy_38.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:15,536 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 38 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:15,550 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 38 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:15,787 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:24,903 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-qtxkj with k8s id: gxy-qtxkj succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:36:25,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 38: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:36:31,890 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 38 finished +galaxy.model.metadata DEBUG 2024-09-03 06:36:31,926 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 38 +galaxy.jobs INFO 2024-09-03 06:36:31,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 38 in /galaxy/server/database/jobs_directory/000/38 +galaxy.jobs DEBUG 2024-09-03 06:36:32,000 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 38 executed (92.979 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:32,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 38 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:36:32,680 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 39 +tpv.core.entities DEBUG 2024-09-03 06:36:32,706 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:36:32,707 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:36:32,711 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:36:32,722 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:36:32,736 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Working directory for job is: /galaxy/server/database/jobs_directory/000/39 +galaxy.jobs.runners DEBUG 2024-09-03 06:36:32,744 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [39] queued (33.477 ms) +galaxy.jobs.handler INFO 2024-09-03 06:36:32,746 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:32,749 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 39 +galaxy.jobs DEBUG 2024-09-03 06:36:32,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [39] prepared (43.023 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:36:32,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:36:32,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:36:32,822 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:36:32,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/39/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/f/9/7/dataset_f97a283f-f08f-4151-8f21-45982b5a59e8.dat' sanger '/galaxy/server/database/objects/9/4/4/dataset_9449b164-f5e1-4ec8-9bff-d3d188a53d37.dat' solexa None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:36:32,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:32,869 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 39 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:36:32,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:36:32,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:36:32,894 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:32,914 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 39 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:33,929 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:36,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-j5mml with k8s id: gxy-j5mml succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:36:37,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 39: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:36:44,011 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 39 finished +galaxy.model.metadata DEBUG 2024-09-03 06:36:44,051 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 39 +galaxy.jobs INFO 2024-09-03 06:36:44,083 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 39 in /galaxy/server/database/jobs_directory/000/39 +galaxy.jobs DEBUG 2024-09-03 06:36:44,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 39 executed (94.146 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:44,137 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 39 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:36:44,939 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 40 +tpv.core.entities DEBUG 2024-09-03 06:36:44,962 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:36:44,962 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:36:44,966 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:36:44,976 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:36:44,987 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Working directory for job is: /galaxy/server/database/jobs_directory/000/40 +galaxy.jobs.runners DEBUG 2024-09-03 06:36:44,993 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [40] queued (26.921 ms) +galaxy.jobs.handler INFO 2024-09-03 06:36:44,995 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:44,998 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 40 +galaxy.jobs DEBUG 2024-09-03 06:36:45,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [40] prepared (70.033 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:36:45,097 [pN:job_handler_0,p:8,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/f/0/1/dataset_f0152540-eb17-448a-bec0-ec271eb6e040_files:/galaxy/server/database/objects/f/0/1/dataset_f0152540-eb17-448a-bec0-ec271eb6e040.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:36:45,107 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:45,121 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 40 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:45,133 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 40 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:46,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:36:55,201 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-cpqpr with k8s id: gxy-cpqpr succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:36:55,325 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 40: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:37:02,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 40 finished +galaxy.model.metadata DEBUG 2024-09-03 06:37:02,457 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 40 +galaxy.jobs INFO 2024-09-03 06:37:02,487 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 40 in /galaxy/server/database/jobs_directory/000/40 +galaxy.jobs DEBUG 2024-09-03 06:37:02,531 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 40 executed (96.854 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:02,545 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 40 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:37:03,280 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 41 +tpv.core.entities DEBUG 2024-09-03 06:37:03,306 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:37:03,307 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:37:03,310 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:37:03,319 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:37:03,332 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Working directory for job is: /galaxy/server/database/jobs_directory/000/41 +galaxy.jobs.runners DEBUG 2024-09-03 06:37:03,339 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [41] queued (29.191 ms) +galaxy.jobs.handler INFO 2024-09-03 06:37:03,341 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:03,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 41 +galaxy.jobs DEBUG 2024-09-03 06:37:03,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [41] prepared (37.456 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:37:03,390 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:37:03,390 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:37:03,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:37:03,432 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/41/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/f/0/1/dataset_f0152540-eb17-448a-bec0-ec271eb6e040.dat' sanger '/galaxy/server/database/objects/a/c/d/dataset_acd596b8-ccd3-45ec-a066-a9ae826baad5.dat' cssanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:37:03,442 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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.runners.kubernetes DEBUG 2024-09-03 06:37:03,459 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 41 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:37:03,467 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:37:03,467 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:37:03,489 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:03,507 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 41 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:04,226 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:07,298 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-t4bpr failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:07,299 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:07,348 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-t4bpr. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:07,357 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 41 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-09-03 06:37:07,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-09-03-06-11-1/jobs/gxy-t4bpr + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-t4bpr": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:07,470 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:07,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (41/gxy-t4bpr) tool_stdout: Groomed 2 sanger reads into cssanger reads. +Based upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2 +Input ASCII range: '!'(33) - '~'(126) +Input decimal range: 0 - 93 + +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:07,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (41/gxy-t4bpr) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:07,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (41/gxy-t4bpr) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:07,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (41/gxy-t4bpr) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-t4bpr. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:07,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Attempting to stop job 41 (gxy-t4bpr) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:07,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Found job with id gxy-t4bpr to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:07,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 41 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:07,570 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (41/gxy-t4bpr) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-09-03 06:37:09,425 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 42 +tpv.core.entities DEBUG 2024-09-03 06:37:09,446 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:37:09,447 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:37:09,450 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:37:09,458 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:37:09,471 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Working directory for job is: /galaxy/server/database/jobs_directory/000/42 +galaxy.jobs.runners DEBUG 2024-09-03 06:37:09,478 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [42] queued (27.785 ms) +galaxy.jobs.handler INFO 2024-09-03 06:37:09,480 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:09,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 42 +galaxy.jobs DEBUG 2024-09-03 06:37:09,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [42] prepared (67.900 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:37:09,575 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/2/d/2/dataset_2d2d892e-bad9-4767-851e-0098b7bb75a5_files:/galaxy/server/database/objects/2/d/2/dataset_2d2d892e-bad9-4767-851e-0098b7bb75a5.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:37:09,584 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (42) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/42/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/42/galaxy_42.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:09,597 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 42 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:09,612 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 42 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:10,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:19,628 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-dnq4l with k8s id: gxy-dnq4l succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:37:19,746 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 42: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:37:26,831 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 42 finished +galaxy.model.metadata DEBUG 2024-09-03 06:37:26,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 42 +galaxy.jobs INFO 2024-09-03 06:37:26,909 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 42 in /galaxy/server/database/jobs_directory/000/42 +galaxy.jobs DEBUG 2024-09-03 06:37:26,951 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 42 executed (100.446 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:26,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 42 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:37:27,800 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 43 +tpv.core.entities DEBUG 2024-09-03 06:37:27,824 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:37:27,824 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:37:27,827 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:37:27,835 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:37:27,847 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Working directory for job is: /galaxy/server/database/jobs_directory/000/43 +galaxy.jobs.runners DEBUG 2024-09-03 06:37:27,854 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [43] queued (27.091 ms) +galaxy.jobs.handler INFO 2024-09-03 06:37:27,856 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:27,858 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 43 +galaxy.jobs DEBUG 2024-09-03 06:37:27,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [43] prepared (41.373 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:37:27,907 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:37:27,907 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:37:28,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:37:28,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/43/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/2/d/2/dataset_2d2d892e-bad9-4767-851e-0098b7bb75a5.dat' solexa '/galaxy/server/database/objects/e/d/5/dataset_ed5dc969-c74f-49c3-a314-d566aeced296.dat' solexa None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:37:28,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (43) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/43/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/43/galaxy_43.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:28,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 43 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:37:28,146 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:37:28,146 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:37:28,165 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:28,185 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 43 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:28,652 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:32,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-7h9c6 with k8s id: gxy-7h9c6 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:37:32,840 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 43: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:37:39,879 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 43 finished +galaxy.model.metadata DEBUG 2024-09-03 06:37:39,920 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 43 +galaxy.jobs INFO 2024-09-03 06:37:39,951 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 43 in /galaxy/server/database/jobs_directory/000/43 +galaxy.jobs DEBUG 2024-09-03 06:37:39,990 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 43 executed (91.596 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:40,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 43 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:37:41,062 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 44 +tpv.core.entities DEBUG 2024-09-03 06:37:41,088 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:37:41,089 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:37:41,092 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:37:41,102 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:37:41,115 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Working directory for job is: /galaxy/server/database/jobs_directory/000/44 +galaxy.jobs.runners DEBUG 2024-09-03 06:37:41,121 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [44] queued (28.880 ms) +galaxy.jobs.handler INFO 2024-09-03 06:37:41,123 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:41,126 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 44 +galaxy.jobs DEBUG 2024-09-03 06:37:41,208 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [44] prepared (75.216 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:37:41,227 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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/7/8/dataset_a78c7ece-c8b8-4d27-99a7-0f935cee9df7_files:/galaxy/server/database/objects/a/7/8/dataset_a78c7ece-c8b8-4d27-99a7-0f935cee9df7.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:37:41,237 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (44) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/44/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/44/galaxy_44.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:41,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 44 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:41,265 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 44 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:41,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:50,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-c5xl7 with k8s id: gxy-c5xl7 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:37:50,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 44: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.runners DEBUG 2024-09-03 06:37:58,121 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 44 finished +galaxy.model.metadata DEBUG 2024-09-03 06:37:58,167 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 44 +galaxy.jobs INFO 2024-09-03 06:37:58,201 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 44 in /galaxy/server/database/jobs_directory/000/44 +galaxy.jobs DEBUG 2024-09-03 06:37:58,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 44 executed (107.544 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:58,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 44 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:37:58,411 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 45 +tpv.core.entities DEBUG 2024-09-03 06:37:58,437 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:37:58,438 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:37:58,442 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:37:58,452 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:37:58,467 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Working directory for job is: /galaxy/server/database/jobs_directory/000/45 +galaxy.jobs.runners DEBUG 2024-09-03 06:37:58,476 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [45] queued (33.608 ms) +galaxy.jobs.handler INFO 2024-09-03 06:37:58,478 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:58,480 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 45 +galaxy.jobs DEBUG 2024-09-03 06:37:58,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [45] prepared (39.511 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:37:58,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:37:58,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:37:58,550 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:37:58,570 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/45/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/a/7/8/dataset_a78c7ece-c8b8-4d27-99a7-0f935cee9df7.dat' solexa '/galaxy/server/database/objects/0/8/c/dataset_08c6d21e-1059-414e-8bbf-2ccafebf50fc.dat' illumina None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:37:58,585 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:58,606 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 45 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:37:58,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:37:58,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:37:58,634 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:58,657 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 45 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:37:58,878 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:02,936 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-rhl5n with k8s id: gxy-rhl5n succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:38:03,063 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 45: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:38:10,106 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 45 finished +galaxy.model.metadata DEBUG 2024-09-03 06:38:10,146 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 45 +galaxy.jobs INFO 2024-09-03 06:38:10,179 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 45 in /galaxy/server/database/jobs_directory/000/45 +galaxy.jobs DEBUG 2024-09-03 06:38:10,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 45 executed (97.463 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:10,235 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 45 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:38:11,774 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 46 +tpv.core.entities DEBUG 2024-09-03 06:38:11,796 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:38:11,797 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:38:11,799 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:38:11,808 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:38:11,821 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Working directory for job is: /galaxy/server/database/jobs_directory/000/46 +galaxy.jobs.runners DEBUG 2024-09-03 06:38:11,829 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [46] queued (29.450 ms) +galaxy.jobs.handler INFO 2024-09-03 06:38:11,831 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:11,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 46 +galaxy.jobs DEBUG 2024-09-03 06:38:11,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [46] prepared (76.100 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:38:11,938 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/46/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/46/registry.xml' '/galaxy/server/database/jobs_directory/000/46/upload_params.json' '46:/galaxy/server/database/objects/e/f/3/dataset_ef35730b-2950-4b83-addf-d621ff7af483_files:/galaxy/server/database/objects/e/f/3/dataset_ef35730b-2950-4b83-addf-d621ff7af483.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:38:11,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (46) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/46/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/46/galaxy_46.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:11,962 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 46 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:11,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 46 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:12,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:22,095 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-phst6 with k8s id: gxy-phst6 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:38:22,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 46: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:38:29,174 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 46 finished +galaxy.model.metadata DEBUG 2024-09-03 06:38:29,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 46 +galaxy.jobs INFO 2024-09-03 06:38:29,254 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 46 in /galaxy/server/database/jobs_directory/000/46 +galaxy.jobs DEBUG 2024-09-03 06:38:29,302 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 46 executed (107.346 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:29,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 46 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:38:30,126 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 47 +tpv.core.entities DEBUG 2024-09-03 06:38:30,152 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:38:30,152 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:38:30,155 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:38:30,168 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:38:30,183 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Working directory for job is: /galaxy/server/database/jobs_directory/000/47 +galaxy.jobs.runners DEBUG 2024-09-03 06:38:30,192 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [47] queued (36.216 ms) +galaxy.jobs.handler INFO 2024-09-03 06:38:30,194 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:30,196 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 47 +galaxy.jobs DEBUG 2024-09-03 06:38:30,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [47] prepared (43.503 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:38:30,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:38:30,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:38:30,269 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:38:30,290 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/47/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/e/f/3/dataset_ef35730b-2950-4b83-addf-d621ff7af483.dat' solexa '/galaxy/server/database/objects/a/7/6/dataset_a76078c0-ecce-4f57-acac-06c3969dc587.dat' sanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:38:30,303 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:30,319 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 47 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:38:30,327 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:38:30,328 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:38:30,346 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:30,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 47 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:31,120 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:35,193 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-n6gm2 with k8s id: gxy-n6gm2 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:38:35,327 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 47: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.runners DEBUG 2024-09-03 06:38:42,347 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 47 finished +galaxy.model.metadata DEBUG 2024-09-03 06:38:42,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 47 +galaxy.jobs INFO 2024-09-03 06:38:42,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 47 in /galaxy/server/database/jobs_directory/000/47 +galaxy.jobs DEBUG 2024-09-03 06:38:42,470 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 47 executed (101.512 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:42,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 47 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:38:43,414 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 48 +tpv.core.entities DEBUG 2024-09-03 06:38:43,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:38:43,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:38:43,438 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:38:43,447 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:38:43,459 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Working directory for job is: /galaxy/server/database/jobs_directory/000/48 +galaxy.jobs.runners DEBUG 2024-09-03 06:38:43,466 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [48] queued (27.663 ms) +galaxy.jobs.handler INFO 2024-09-03 06:38:43,468 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:43,471 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 48 +galaxy.jobs DEBUG 2024-09-03 06:38:43,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [48] prepared (67.510 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:38:43,564 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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/7/e/1/dataset_7e1e85a9-9ed2-46f2-8b89-3f776375cd29_files:/galaxy/server/database/objects/7/e/1/dataset_7e1e85a9-9ed2-46f2-8b89-3f776375cd29.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:38:43,572 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (48) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/48/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/48/galaxy_48.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:43,587 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 48 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:43,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 48 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:44,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:52,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-q5htl with k8s id: gxy-q5htl succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:38:52,457 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 48: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.runners DEBUG 2024-09-03 06:38:59,559 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 48 finished +galaxy.model.metadata DEBUG 2024-09-03 06:38:59,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 48 +galaxy.jobs INFO 2024-09-03 06:38:59,639 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 48 in /galaxy/server/database/jobs_directory/000/48 +galaxy.jobs DEBUG 2024-09-03 06:38:59,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 48 executed (103.529 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:38:59,700 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 48 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:39:00,746 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 49 +tpv.core.entities DEBUG 2024-09-03 06:39:00,773 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:39:00,774 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:39:00,778 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:39:00,790 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:39:00,805 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Working directory for job is: /galaxy/server/database/jobs_directory/000/49 +galaxy.jobs.runners DEBUG 2024-09-03 06:39:00,814 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [49] queued (36.041 ms) +galaxy.jobs.handler INFO 2024-09-03 06:39:00,816 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:00,818 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 49 +galaxy.jobs DEBUG 2024-09-03 06:39:00,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [49] prepared (42.982 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:39:00,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:39:00,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:39:00,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:39:00,912 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/49/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/7/e/1/dataset_7e1e85a9-9ed2-46f2-8b89-3f776375cd29.dat' solexa '/galaxy/server/database/objects/7/f/8/dataset_7f8e6fb2-8c43-41d1-8f3f-9579f05309f1.dat' cssanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:39:00,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (49) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/49/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/49/galaxy_49.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:00,938 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 49 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:39:00,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:39:00,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:39:00,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:00,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 49 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:01,355 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:05,414 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-xcm4m with k8s id: gxy-xcm4m succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:39:05,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 49: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:39:12,604 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 49 finished +galaxy.model.metadata DEBUG 2024-09-03 06:39:12,643 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 49 +galaxy.jobs INFO 2024-09-03 06:39:12,676 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 49 in /galaxy/server/database/jobs_directory/000/49 +galaxy.jobs DEBUG 2024-09-03 06:39:12,723 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 49 executed (100.387 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:12,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 49 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:39:14,021 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 50 +tpv.core.entities DEBUG 2024-09-03 06:39:14,043 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:39:14,044 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:39:14,048 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:39:14,057 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:39:14,068 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Working directory for job is: /galaxy/server/database/jobs_directory/000/50 +galaxy.jobs.runners DEBUG 2024-09-03 06:39:14,074 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [50] queued (25.773 ms) +galaxy.jobs.handler INFO 2024-09-03 06:39:14,076 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:14,078 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 50 +galaxy.jobs DEBUG 2024-09-03 06:39:14,159 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [50] prepared (73.429 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:39:14,178 [pN:job_handler_0,p:8,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/a/0/9/dataset_a094c793-d2ba-4dd4-a923-37aa5b938c31_files:/galaxy/server/database/objects/a/0/9/dataset_a094c793-d2ba-4dd4-a923-37aa5b938c31.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:39:14,188 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:14,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 50 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:14,217 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 50 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:14,436 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:23,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-tq559 with k8s id: gxy-tq559 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:39:23,690 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 50: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:39:30,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 50 finished +galaxy.model.metadata DEBUG 2024-09-03 06:39:30,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 50 +galaxy.jobs INFO 2024-09-03 06:39:30,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 50 in /galaxy/server/database/jobs_directory/000/50 +galaxy.jobs DEBUG 2024-09-03 06:39:30,919 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 50 executed (95.594 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:30,931 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 50 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:39:31,466 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 51 +tpv.core.entities DEBUG 2024-09-03 06:39:31,493 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:39:31,493 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:39:31,497 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:39:31,507 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:39:31,523 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Working directory for job is: /galaxy/server/database/jobs_directory/000/51 +galaxy.jobs.runners DEBUG 2024-09-03 06:39:31,532 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [51] queued (34.696 ms) +galaxy.jobs.handler INFO 2024-09-03 06:39:31,534 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:31,536 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 51 +galaxy.jobs DEBUG 2024-09-03 06:39:31,579 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [51] prepared (37.346 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:39:31,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:39:31,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:39:31,603 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:39:31,625 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/51/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/a/0/9/dataset_a094c793-d2ba-4dd4-a923-37aa5b938c31.dat' cssanger '/galaxy/server/database/objects/2/4/1/dataset_2411f8ca-8095-4ca6-b237-15b7f45b5933.dat' cssanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:39:31,638 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (51) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/51/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/51/galaxy_51.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:31,656 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 51 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:39:31,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:39:31,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:39:31,684 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:31,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 51 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:32,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:35,628 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-4s55p with k8s id: gxy-4s55p succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:39:35,751 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 51: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:39:42,647 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 51 finished +galaxy.model.metadata DEBUG 2024-09-03 06:39:42,681 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 51 +galaxy.jobs INFO 2024-09-03 06:39:42,715 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 51 in /galaxy/server/database/jobs_directory/000/51 +galaxy.jobs DEBUG 2024-09-03 06:39:42,757 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 51 executed (93.135 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:42,771 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 51 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:39:43,726 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 52 +tpv.core.entities DEBUG 2024-09-03 06:39:43,749 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:39:43,749 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:39:43,753 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:39:43,763 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:39:43,778 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Working directory for job is: /galaxy/server/database/jobs_directory/000/52 +galaxy.jobs.runners DEBUG 2024-09-03 06:39:43,785 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [52] queued (32.633 ms) +galaxy.jobs.handler INFO 2024-09-03 06:39:43,787 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:43,790 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 52 +galaxy.jobs DEBUG 2024-09-03 06:39:43,869 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [52] prepared (70.626 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:39:43,888 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/52/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/52/registry.xml' '/galaxy/server/database/jobs_directory/000/52/upload_params.json' '52:/galaxy/server/database/objects/0/c/8/dataset_0c822b25-84a1-43b6-b86c-353817fe5f1f_files:/galaxy/server/database/objects/0/c/8/dataset_0c822b25-84a1-43b6-b86c-353817fe5f1f.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:39:43,897 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (52) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/52/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/52/galaxy_52.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:43,911 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 52 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:43,924 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 52 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:44,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:39:53,880 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ss9wt with k8s id: gxy-ss9wt succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:39:53,997 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 52: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:40:01,177 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 52 finished +galaxy.model.metadata DEBUG 2024-09-03 06:40:01,218 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 52 +galaxy.jobs INFO 2024-09-03 06:40:01,247 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 52 in /galaxy/server/database/jobs_directory/000/52 +galaxy.jobs DEBUG 2024-09-03 06:40:01,301 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 52 executed (104.430 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:01,312 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 52 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:40:02,073 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 53 +tpv.core.entities DEBUG 2024-09-03 06:40:02,098 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:40:02,099 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:40:02,102 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:40:02,112 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:40:02,125 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Working directory for job is: /galaxy/server/database/jobs_directory/000/53 +galaxy.jobs.runners DEBUG 2024-09-03 06:40:02,135 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [53] queued (32.928 ms) +galaxy.jobs.handler INFO 2024-09-03 06:40:02,137 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:02,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 53 +galaxy.jobs DEBUG 2024-09-03 06:40:02,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [53] prepared (45.834 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:40:02,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:40:02,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:40:02,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:40:02,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/53/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/0/c/8/dataset_0c822b25-84a1-43b6-b86c-353817fe5f1f.dat' cssanger '/galaxy/server/database/objects/2/0/4/dataset_20464c28-d355-4e86-808f-5637246b7ea3.dat' sanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:40:02,252 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (53) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/53/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/53/galaxy_53.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:02,267 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 53 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:40:02,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:40:02,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:40:02,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:02,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 53 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:02,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:06,968 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-lmncn with k8s id: gxy-lmncn succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:40:07,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 53: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-03 06:40:14,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 53 finished +galaxy.model.metadata DEBUG 2024-09-03 06:40:14,154 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 53 +galaxy.jobs INFO 2024-09-03 06:40:14,187 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 53 in /galaxy/server/database/jobs_directory/000/53 +galaxy.jobs DEBUG 2024-09-03 06:40:14,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 53 executed (96.768 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:14,243 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 53 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:40:15,364 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 54 +tpv.core.entities DEBUG 2024-09-03 06:40:15,388 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:40:15,388 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:40:15,391 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:40:15,401 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:40:15,415 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Working directory for job is: /galaxy/server/database/jobs_directory/000/54 +galaxy.jobs.runners DEBUG 2024-09-03 06:40:15,422 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [54] queued (31.096 ms) +galaxy.jobs.handler INFO 2024-09-03 06:40:15,425 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:15,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 54 +galaxy.jobs DEBUG 2024-09-03 06:40:15,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [54] prepared (79.534 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:40:15,533 [pN:job_handler_0,p:8,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/7/f/d/dataset_7fd3ddf3-ca20-4078-a452-7b6d02addf4c_files:/galaxy/server/database/objects/7/f/d/dataset_7fd3ddf3-ca20-4078-a452-7b6d02addf4c.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:40:15,543 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:15,557 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 54 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:15,571 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 54 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:15,991 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:25,126 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-88j28 with k8s id: gxy-88j28 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:40:25,270 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 54: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:40:32,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 54 finished +galaxy.model.metadata DEBUG 2024-09-03 06:40:32,467 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 54 +galaxy.jobs INFO 2024-09-03 06:40:32,505 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 54 in /galaxy/server/database/jobs_directory/000/54 +galaxy.jobs DEBUG 2024-09-03 06:40:32,560 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 54 executed (118.109 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:32,572 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 54 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:40:33,728 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 55 +tpv.core.entities DEBUG 2024-09-03 06:40:33,760 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:40:33,760 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:40:33,765 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:40:33,780 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:40:33,796 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Working directory for job is: /galaxy/server/database/jobs_directory/000/55 +galaxy.jobs.runners DEBUG 2024-09-03 06:40:33,805 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [55] queued (39.650 ms) +galaxy.jobs.handler INFO 2024-09-03 06:40:33,808 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:33,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 55 +galaxy.jobs DEBUG 2024-09-03 06:40:33,866 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [55] prepared (46.274 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:40:33,866 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:40:33,866 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:40:33,894 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:40:33,919 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/55/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/7/f/d/dataset_7fd3ddf3-ca20-4078-a452-7b6d02addf4c.dat' cssanger '/galaxy/server/database/objects/9/b/d/dataset_9bdee107-8099-47db-82b6-4b380741bc7b.dat' illumina None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:40:33,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (55) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/55/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/55/galaxy_55.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:33,949 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 55 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:40:33,957 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:40:33,957 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:40:33,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:33,998 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 55 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:34,150 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:38,239 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-9xszj with k8s id: gxy-9xszj succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:40:38,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 55: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:40:45,408 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 55 finished +galaxy.model.metadata DEBUG 2024-09-03 06:40:45,445 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 55 +galaxy.jobs INFO 2024-09-03 06:40:45,477 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 55 in /galaxy/server/database/jobs_directory/000/55 +galaxy.jobs DEBUG 2024-09-03 06:40:45,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 55 executed (87.515 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:45,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 55 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:40:47,085 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 56 +tpv.core.entities DEBUG 2024-09-03 06:40:47,108 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:40:47,108 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:40:47,112 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:40:47,123 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:40:47,138 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Working directory for job is: /galaxy/server/database/jobs_directory/000/56 +galaxy.jobs.runners DEBUG 2024-09-03 06:40:47,145 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [56] queued (33.254 ms) +galaxy.jobs.handler INFO 2024-09-03 06:40:47,147 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:47,149 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 56 +galaxy.jobs DEBUG 2024-09-03 06:40:47,229 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [56] prepared (71.236 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:40:47,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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/c/3/dataset_fc368bde-3f7a-4f2c-9693-63c96fe7d3e3_files:/galaxy/server/database/objects/f/c/3/dataset_fc368bde-3f7a-4f2c-9693-63c96fe7d3e3.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:40:47,258 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:47,272 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 56 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:47,285 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 56 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:48,269 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:40:57,395 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-hb7sg with k8s id: gxy-hb7sg succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:40:57,519 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 56: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:41:04,567 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 56 finished +galaxy.model.metadata DEBUG 2024-09-03 06:41:04,611 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 56 +galaxy.jobs INFO 2024-09-03 06:41:04,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 56 in /galaxy/server/database/jobs_directory/000/56 +galaxy.jobs DEBUG 2024-09-03 06:41:04,699 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 56 executed (112.698 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:04,711 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 56 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:41:05,444 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 57 +tpv.core.entities DEBUG 2024-09-03 06:41:05,468 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:41:05,468 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:41:05,471 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:41:05,480 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:41:05,494 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Working directory for job is: /galaxy/server/database/jobs_directory/000/57 +galaxy.jobs.runners DEBUG 2024-09-03 06:41:05,502 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [57] queued (30.985 ms) +galaxy.jobs.handler INFO 2024-09-03 06:41:05,505 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:05,507 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 57 +galaxy.jobs DEBUG 2024-09-03 06:41:05,558 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [57] prepared (42.431 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:41:05,558 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:41:05,558 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:41:05,577 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:41:05,599 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/57/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/f/c/3/dataset_fc368bde-3f7a-4f2c-9693-63c96fe7d3e3.dat' cssanger '/galaxy/server/database/objects/e/4/2/dataset_e42f9f92-4d00-403c-86d7-ff4079519f41.dat' solexa None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:41:05,613 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (57) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/57/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/57/galaxy_57.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:05,632 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 57 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:41:05,640 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:41:05,641 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:41:05,678 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:05,700 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 57 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:06,422 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:10,483 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-8nb8r with k8s id: gxy-8nb8r succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:41:10,599 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 57: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:41:17,592 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 57 finished +galaxy.model.metadata DEBUG 2024-09-03 06:41:17,633 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 57 +galaxy.jobs INFO 2024-09-03 06:41:17,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 57 in /galaxy/server/database/jobs_directory/000/57 +galaxy.jobs DEBUG 2024-09-03 06:41:17,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 57 executed (108.315 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:17,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 57 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:41:18,726 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 58 +tpv.core.entities DEBUG 2024-09-03 06:41:18,750 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:41:18,750 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:41:18,754 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:41:18,765 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:41:18,779 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Working directory for job is: /galaxy/server/database/jobs_directory/000/58 +galaxy.jobs.runners DEBUG 2024-09-03 06:41:18,785 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [58] queued (31.381 ms) +galaxy.jobs.handler INFO 2024-09-03 06:41:18,788 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:18,790 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 58 +galaxy.jobs DEBUG 2024-09-03 06:41:18,865 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [58] prepared (68.333 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:41:18,882 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/58/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/58/registry.xml' '/galaxy/server/database/jobs_directory/000/58/upload_params.json' '58:/galaxy/server/database/objects/2/1/8/dataset_218ad061-7e1d-4a6e-b43c-71d24feb34eb_files:/galaxy/server/database/objects/2/1/8/dataset_218ad061-7e1d-4a6e-b43c-71d24feb34eb.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:41:18,890 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (58) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/58/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/58/galaxy_58.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:18,903 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 58 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:18,915 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 58 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:19,511 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:28,652 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ddkcg with k8s id: gxy-ddkcg succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:41:28,775 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 58: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:41:35,705 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 58 finished +galaxy.model.metadata DEBUG 2024-09-03 06:41:35,774 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 58 +galaxy.jobs INFO 2024-09-03 06:41:35,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 58 in /galaxy/server/database/jobs_directory/000/58 +galaxy.jobs DEBUG 2024-09-03 06:41:35,873 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 58 executed (150.712 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:35,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 58 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:41:36,060 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 59 +tpv.core.entities DEBUG 2024-09-03 06:41:36,082 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:41:36,083 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:41:36,087 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:41:36,096 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:41:36,110 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Working directory for job is: /galaxy/server/database/jobs_directory/000/59 +galaxy.jobs.runners DEBUG 2024-09-03 06:41:36,118 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [59] queued (30.812 ms) +galaxy.jobs.handler INFO 2024-09-03 06:41:36,119 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:36,122 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 59 +galaxy.jobs DEBUG 2024-09-03 06:41:36,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [59] prepared (44.464 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:41:36,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:41:36,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:41:36,197 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:41:36,218 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/59/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/2/1/8/dataset_218ad061-7e1d-4a6e-b43c-71d24feb34eb.dat' cssanger '/galaxy/server/database/objects/1/f/0/dataset_1f0b858b-c19e-4e75-a902-806e864e02c3.dat' cssanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:41:36,229 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (59) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/59/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/59/galaxy_59.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:36,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 59 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:41:36,252 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:41:36,252 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:41:36,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:36,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 59 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:36,684 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:40,752 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-qphm8 with k8s id: gxy-qphm8 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:41:40,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 59: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:41:47,948 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 59 finished +galaxy.model.metadata DEBUG 2024-09-03 06:41:47,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 59 +galaxy.jobs INFO 2024-09-03 06:41:48,021 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 59 in /galaxy/server/database/jobs_directory/000/59 +galaxy.jobs DEBUG 2024-09-03 06:41:48,062 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 59 executed (94.387 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:48,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 59 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:41:49,341 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 60 +tpv.core.entities DEBUG 2024-09-03 06:41:49,365 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:41:49,365 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:41:49,369 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:41:49,378 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:41:49,391 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Working directory for job is: /galaxy/server/database/jobs_directory/000/60 +galaxy.jobs.runners DEBUG 2024-09-03 06:41:49,398 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [60] queued (28.767 ms) +galaxy.jobs.handler INFO 2024-09-03 06:41:49,400 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:49,402 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 60 +galaxy.jobs DEBUG 2024-09-03 06:41:49,493 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [60] prepared (82.431 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:41:49,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/60/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/60/registry.xml' '/galaxy/server/database/jobs_directory/000/60/upload_params.json' '60:/galaxy/server/database/objects/a/4/e/dataset_a4e43699-5406-4ad9-946a-188e66b004af_files:/galaxy/server/database/objects/a/4/e/dataset_a4e43699-5406-4ad9-946a-188e66b004af.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:41:49,522 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (60) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/60/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/60/galaxy_60.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:49,537 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 60 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:49,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 60 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:49,781 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:41:58,979 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-kbsgh with k8s id: gxy-kbsgh succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:41:59,103 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 60: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:42:06,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 60 finished +galaxy.model.metadata DEBUG 2024-09-03 06:42:06,326 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 60 +galaxy.jobs INFO 2024-09-03 06:42:06,360 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 60 in /galaxy/server/database/jobs_directory/000/60 +galaxy.jobs DEBUG 2024-09-03 06:42:06,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 60 executed (108.090 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:06,424 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 60 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:42:07,704 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 61 +tpv.core.entities DEBUG 2024-09-03 06:42:07,726 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:42:07,727 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:42:07,730 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:42:07,739 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:42:07,754 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Working directory for job is: /galaxy/server/database/jobs_directory/000/61 +galaxy.jobs.runners DEBUG 2024-09-03 06:42:07,763 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [61] queued (32.098 ms) +galaxy.jobs.handler INFO 2024-09-03 06:42:07,765 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:07,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 61 +galaxy.jobs DEBUG 2024-09-03 06:42:07,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [61] prepared (42.878 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:42:07,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:42:07,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:42:07,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:42:07,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/61/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/a/4/e/dataset_a4e43699-5406-4ad9-946a-188e66b004af.dat' sanger '/galaxy/server/database/objects/0/b/c/dataset_0bc95472-690f-480d-9241-24495656acdb.dat' sanger None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:42:07,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (61) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/61/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/61/galaxy_61.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:07,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 61 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:42:07,899 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:42:07,899 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:42:07,918 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:07,938 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 61 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:09,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:13,092 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-vhh27 with k8s id: gxy-vhh27 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:42:13,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 61: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:42:20,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 61 finished +galaxy.model.metadata DEBUG 2024-09-03 06:42:20,253 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 61 +galaxy.jobs INFO 2024-09-03 06:42:20,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 61 in /galaxy/server/database/jobs_directory/000/61 +galaxy.jobs DEBUG 2024-09-03 06:42:20,328 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 61 executed (92.626 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:20,340 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 61 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:42:21,990 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 62 +tpv.core.entities DEBUG 2024-09-03 06:42:22,014 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:42:22,014 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:42:22,018 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:42:22,030 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:42:22,043 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Working directory for job is: /galaxy/server/database/jobs_directory/000/62 +galaxy.jobs.runners DEBUG 2024-09-03 06:42:22,051 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [62] queued (32.542 ms) +galaxy.jobs.handler INFO 2024-09-03 06:42:22,053 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:22,055 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 62 +galaxy.jobs DEBUG 2024-09-03 06:42:22,136 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [62] prepared (74.332 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:42:22,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/62/tool_script.sh] for tool command [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' '62:/galaxy/server/database/objects/b/f/c/dataset_bfc09b58-9235-4389-a35f-2d6ba8fecc74_files:/galaxy/server/database/objects/b/f/c/dataset_bfc09b58-9235-4389-a35f-2d6ba8fecc74.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:42:22,165 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (62) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/62/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/62/galaxy_62.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:22,179 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 62 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:22,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 62 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:23,135 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:31,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-cgjdv with k8s id: gxy-cgjdv succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:42:31,365 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 62: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:42:38,374 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 62 finished +galaxy.model.metadata DEBUG 2024-09-03 06:42:38,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 62 +galaxy.jobs INFO 2024-09-03 06:42:38,454 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 62 in /galaxy/server/database/jobs_directory/000/62 +galaxy.jobs DEBUG 2024-09-03 06:42:38,500 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 62 executed (105.129 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:38,514 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 62 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:42:39,334 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 63 +tpv.core.entities DEBUG 2024-09-03 06:42:39,360 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:42:39,360 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:42:39,363 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:42:39,373 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:42:39,385 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Working directory for job is: /galaxy/server/database/jobs_directory/000/63 +galaxy.jobs.runners DEBUG 2024-09-03 06:42:39,394 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [63] queued (30.153 ms) +galaxy.jobs.handler INFO 2024-09-03 06:42:39,396 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:39,398 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 63 +galaxy.jobs DEBUG 2024-09-03 06:42:39,443 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [63] prepared (37.372 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:42:39,443 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:42:39,443 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:42:39,635 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:42:39,656 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/63/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/b/f/c/dataset_bfc09b58-9235-4389-a35f-2d6ba8fecc74.dat' sanger '/galaxy/server/database/objects/d/3/c/dataset_d3c61163-1392-42c9-a008-1eccb3d16cd8.dat' illumina None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:42:39,667 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:39,684 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 63 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:42:39,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:42:39,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:42:39,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:39,726 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 63 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:40,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:44,321 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-cxvbm with k8s id: gxy-cxvbm succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:42:44,459 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 63: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:42:51,545 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 63 finished +galaxy.model.metadata DEBUG 2024-09-03 06:42:51,586 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 63 +galaxy.jobs INFO 2024-09-03 06:42:51,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 63 in /galaxy/server/database/jobs_directory/000/63 +galaxy.jobs DEBUG 2024-09-03 06:42:51,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 63 executed (95.126 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:51,675 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 63 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:42:52,619 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 64 +tpv.core.entities DEBUG 2024-09-03 06:42:52,640 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:42:52,640 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:42:52,644 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:42:52,654 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:42:52,667 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Working directory for job is: /galaxy/server/database/jobs_directory/000/64 +galaxy.jobs.runners DEBUG 2024-09-03 06:42:52,673 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [64] queued (29.296 ms) +galaxy.jobs.handler INFO 2024-09-03 06:42:52,675 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:52,677 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 64 +galaxy.jobs DEBUG 2024-09-03 06:42:52,762 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [64] prepared (76.411 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:42:52,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/64/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/64/registry.xml' '/galaxy/server/database/jobs_directory/000/64/upload_params.json' '64:/galaxy/server/database/objects/a/c/a/dataset_aca73cd3-7579-45a7-bf41-bb3a3703d62f_files:/galaxy/server/database/objects/a/c/a/dataset_aca73cd3-7579-45a7-bf41-bb3a3703d62f.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:42:52,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (64) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/64/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/64/galaxy_64.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:52,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 64 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:52,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 64 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:42:53,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:02,458 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-qnkfp with k8s id: gxy-qnkfp succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:43:02,578 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 64: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:43:09,576 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 64 finished +galaxy.model.metadata DEBUG 2024-09-03 06:43:09,620 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 64 +galaxy.jobs INFO 2024-09-03 06:43:09,648 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 64 in /galaxy/server/database/jobs_directory/000/64 +galaxy.jobs DEBUG 2024-09-03 06:43:09,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 64 executed (95.989 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:09,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 64 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:43:09,952 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 65 +tpv.core.entities DEBUG 2024-09-03 06:43:09,974 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:43:09,974 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:43:09,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:43:09,985 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:43:09,995 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Working directory for job is: /galaxy/server/database/jobs_directory/000/65 +galaxy.jobs.runners DEBUG 2024-09-03 06:43:10,001 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [65] queued (24.213 ms) +galaxy.jobs.handler INFO 2024-09-03 06:43:10,003 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:10,006 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 65 +galaxy.jobs DEBUG 2024-09-03 06:43:10,054 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [65] prepared (40.863 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:43:10,055 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:43:10,055 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:43:10,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:43:10,095 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/65/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/a/c/a/dataset_aca73cd3-7579-45a7-bf41-bb3a3703d62f.dat' sanger '/galaxy/server/database/objects/d/5/b/dataset_d5bb9c58-64b0-44b8-84ed-7eb06e61ee69.dat' solexa None summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:43:10,107 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (65) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/65/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/65/galaxy_65.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:10,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 65 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:43:10,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:43:10,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:43:10,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:10,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 65 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:10,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:14,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ww75w with k8s id: gxy-ww75w succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:43:14,680 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 65: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:43:21,730 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 65 finished +galaxy.model.metadata DEBUG 2024-09-03 06:43:21,770 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 65 +galaxy.jobs INFO 2024-09-03 06:43:21,804 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 65 in /galaxy/server/database/jobs_directory/000/65 +galaxy.jobs DEBUG 2024-09-03 06:43:21,849 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 65 executed (99.460 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:21,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 65 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:43:23,218 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 66 +tpv.core.entities DEBUG 2024-09-03 06:43:23,242 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:43:23,243 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:43:23,246 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:43:23,257 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:43:23,270 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Working directory for job is: /galaxy/server/database/jobs_directory/000/66 +galaxy.jobs.runners DEBUG 2024-09-03 06:43:23,277 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [66] queued (30.937 ms) +galaxy.jobs.handler INFO 2024-09-03 06:43:23,280 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:23,281 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 66 +galaxy.jobs DEBUG 2024-09-03 06:43:23,359 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [66] prepared (71.268 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:43:23,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/66/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/66/registry.xml' '/galaxy/server/database/jobs_directory/000/66/upload_params.json' '66:/galaxy/server/database/objects/0/9/9/dataset_099aafb9-a013-477d-8b8d-49e6497454a5_files:/galaxy/server/database/objects/0/9/9/dataset_099aafb9-a013-477d-8b8d-49e6497454a5.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:43:23,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (66) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/66/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/66/galaxy_66.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:23,402 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 66 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:23,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 66 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:23,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:32,684 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-tpj5m with k8s id: gxy-tpj5m succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:43:32,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 66: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:43:39,816 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 66 finished +galaxy.model.metadata DEBUG 2024-09-03 06:43:39,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 66 +galaxy.jobs INFO 2024-09-03 06:43:39,881 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 66 in /galaxy/server/database/jobs_directory/000/66 +galaxy.jobs DEBUG 2024-09-03 06:43:39,923 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 66 executed (89.478 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:39,936 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 66 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:43:40,562 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 67 +tpv.core.entities DEBUG 2024-09-03 06:43:40,587 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:43:40,587 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:43:40,591 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:43:40,601 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:43:40,613 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Working directory for job is: /galaxy/server/database/jobs_directory/000/67 +galaxy.jobs.runners DEBUG 2024-09-03 06:43:40,621 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [67] queued (29.497 ms) +galaxy.jobs.handler INFO 2024-09-03 06:43:40,623 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:40,624 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 67 +galaxy.jobs DEBUG 2024-09-03 06:43:40,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [67] prepared (32.317 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:43:40,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:43:40,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:43:40,683 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:43:40,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/67/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/0/9/9/dataset_099aafb9-a013-477d-8b8d-49e6497454a5.dat' sanger '/galaxy/server/database/objects/f/8/6/dataset_f863c469-cb02-4fbd-87d9-3c1cada97c48.dat' sanger ascii summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:43:40,714 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:40,728 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 67 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:43:40,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:43:40,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:43:40,750 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:40,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 67 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:41,710 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:45,771 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-bn9lg with k8s id: gxy-bn9lg succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:43:45,880 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 67: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:43:52,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 67 finished +galaxy.model.metadata DEBUG 2024-09-03 06:43:52,777 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 67 +galaxy.jobs INFO 2024-09-03 06:43:52,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 67 in /galaxy/server/database/jobs_directory/000/67 +galaxy.jobs DEBUG 2024-09-03 06:43:52,862 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 67 executed (106.589 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:52,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 67 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:43:53,835 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 68 +tpv.core.entities DEBUG 2024-09-03 06:43:53,858 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:43:53,858 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:43:53,861 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:43:53,871 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:43:53,885 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Working directory for job is: /galaxy/server/database/jobs_directory/000/68 +galaxy.jobs.runners DEBUG 2024-09-03 06:43:53,891 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [68] queued (29.336 ms) +galaxy.jobs.handler INFO 2024-09-03 06:43:53,893 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:53,895 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 68 +galaxy.jobs DEBUG 2024-09-03 06:43:53,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [68] prepared (73.920 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:43:53,996 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/68/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/68/registry.xml' '/galaxy/server/database/jobs_directory/000/68/upload_params.json' '68:/galaxy/server/database/objects/0/f/b/dataset_0fbfd951-f3ba-450a-8e5d-333f3a57ce89_files:/galaxy/server/database/objects/0/f/b/dataset_0fbfd951-f3ba-450a-8e5d-333f3a57ce89.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:43:54,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (68) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/68/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/68/galaxy_68.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:54,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 68 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:54,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 68 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:43:54,795 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:03,916 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-k2nkm with k8s id: gxy-k2nkm succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:44:04,036 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 68: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:44:11,256 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 68 finished +galaxy.model.metadata DEBUG 2024-09-03 06:44:11,309 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 68 +galaxy.jobs INFO 2024-09-03 06:44:11,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 68 in /galaxy/server/database/jobs_directory/000/68 +galaxy.jobs DEBUG 2024-09-03 06:44:11,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 68 executed (109.103 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:11,401 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 68 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:44:12,206 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 69 +tpv.core.entities DEBUG 2024-09-03 06:44:12,233 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:44:12,233 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:44:12,236 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:44:12,244 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:44:12,257 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Working directory for job is: /galaxy/server/database/jobs_directory/000/69 +galaxy.jobs.runners DEBUG 2024-09-03 06:44:12,266 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [69] queued (29.255 ms) +galaxy.jobs.handler INFO 2024-09-03 06:44:12,268 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:12,271 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 69 +galaxy.jobs DEBUG 2024-09-03 06:44:12,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [69] prepared (37.256 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:44:12,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:44:12,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:44:12,339 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:44:12,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/69/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/0/f/b/dataset_0fbfd951-f3ba-450a-8e5d-333f3a57ce89.dat' sanger '/galaxy/server/database/objects/e/b/c/dataset_ebc5eebc-b0b8-4d5e-b11d-f5bc11b14d82.dat' sanger decimal summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:44:12,370 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (69) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/69/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/69/galaxy_69.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:12,386 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 69 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:44:12,396 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:44:12,396 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:44:12,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:12,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 69 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:12,939 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:16,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-n72zt with k8s id: gxy-n72zt succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:44:17,131 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 69: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:44:23,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 69 finished +galaxy.model.metadata DEBUG 2024-09-03 06:44:23,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 69 +galaxy.jobs INFO 2024-09-03 06:44:24,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 69 in /galaxy/server/database/jobs_directory/000/69 +galaxy.jobs DEBUG 2024-09-03 06:44:24,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 69 executed (91.747 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:24,071 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 69 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:44:25,477 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 70 +tpv.core.entities DEBUG 2024-09-03 06:44:25,501 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:44:25,501 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:44:25,505 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:44:25,514 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:44:25,528 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Working directory for job is: /galaxy/server/database/jobs_directory/000/70 +galaxy.jobs.runners DEBUG 2024-09-03 06:44:25,535 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [70] queued (29.752 ms) +galaxy.jobs.handler INFO 2024-09-03 06:44:25,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:25,539 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 70 +galaxy.jobs DEBUG 2024-09-03 06:44:25,624 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [70] prepared (76.524 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:44:25,643 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/70/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/70/registry.xml' '/galaxy/server/database/jobs_directory/000/70/upload_params.json' '70:/galaxy/server/database/objects/0/d/9/dataset_0d9ab7ef-9518-4643-bb40-24562d364f77_files:/galaxy/server/database/objects/0/d/9/dataset_0d9ab7ef-9518-4643-bb40-24562d364f77.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:44:25,668 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (70) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/70/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/70/galaxy_70.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:25,684 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 70 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:25,698 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 70 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:26,022 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:36,167 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-c62td with k8s id: gxy-c62td succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:44:36,286 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 70: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:44:43,199 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 70 finished +galaxy.model.metadata DEBUG 2024-09-03 06:44:43,242 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 70 +galaxy.jobs INFO 2024-09-03 06:44:43,278 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 70 in /galaxy/server/database/jobs_directory/000/70 +galaxy.jobs DEBUG 2024-09-03 06:44:43,327 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 70 executed (108.040 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:43,338 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 70 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:44:43,800 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 71 +tpv.core.entities DEBUG 2024-09-03 06:44:43,821 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:44:43,821 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:44:43,824 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:44:43,832 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:44:43,843 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Working directory for job is: /galaxy/server/database/jobs_directory/000/71 +galaxy.jobs.runners DEBUG 2024-09-03 06:44:43,849 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [71] queued (25.314 ms) +galaxy.jobs.handler INFO 2024-09-03 06:44:43,851 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:43,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 71 +galaxy.jobs DEBUG 2024-09-03 06:44:43,897 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [71] prepared (36.864 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:44:43,898 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:44:43,898 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:44:43,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:44:43,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/71/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/0/d/9/dataset_0d9ab7ef-9518-4643-bb40-24562d364f77.dat' sanger '/galaxy/server/database/objects/7/7/d/dataset_77d89291-b1f2-445b-b037-2d8a75d3c1f6.dat' sanger ascii summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:44:43,947 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:43,964 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 71 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:44:43,969 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:44:43,969 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:44:43,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:44,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 71 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:44,193 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:48,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-68pfn with k8s id: gxy-68pfn succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:44:48,373 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 71: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:44:55,171 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 71 finished +galaxy.model.metadata DEBUG 2024-09-03 06:44:55,211 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 71 +galaxy.jobs INFO 2024-09-03 06:44:55,239 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 71 in /galaxy/server/database/jobs_directory/000/71 +galaxy.jobs DEBUG 2024-09-03 06:44:55,284 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 71 executed (92.270 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:55,299 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 71 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:44:56,073 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 72 +tpv.core.entities DEBUG 2024-09-03 06:44:56,093 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:44:56,093 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:44:56,096 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:44:56,103 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:44:56,115 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Working directory for job is: /galaxy/server/database/jobs_directory/000/72 +galaxy.jobs.runners DEBUG 2024-09-03 06:44:56,121 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [72] queued (25.265 ms) +galaxy.jobs.handler INFO 2024-09-03 06:44:56,125 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:56,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 72 +galaxy.jobs DEBUG 2024-09-03 06:44:56,206 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [72] prepared (72.047 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:44:56,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/72/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/72/registry.xml' '/galaxy/server/database/jobs_directory/000/72/upload_params.json' '72:/galaxy/server/database/objects/b/8/0/dataset_b80482de-c2c8-405d-852f-584e16048d2f_files:/galaxy/server/database/objects/b/8/0/dataset_b80482de-c2c8-405d-852f-584e16048d2f.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:44:56,234 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (72) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/72/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/72/galaxy_72.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:56,247 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 72 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:56,259 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 72 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:44:57,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:06,393 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-zpg9b with k8s id: gxy-zpg9b succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:45:06,517 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 72: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:45:13,480 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 72 finished +galaxy.model.metadata DEBUG 2024-09-03 06:45:13,520 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 72 +galaxy.jobs INFO 2024-09-03 06:45:13,553 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 72 in /galaxy/server/database/jobs_directory/000/72 +galaxy.jobs DEBUG 2024-09-03 06:45:13,603 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 72 executed (102.287 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:13,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 72 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:45:14,408 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 73 +tpv.core.entities DEBUG 2024-09-03 06:45:14,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:45:14,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:45:14,439 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:45:14,451 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:45:14,466 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Working directory for job is: /galaxy/server/database/jobs_directory/000/73 +galaxy.jobs.runners DEBUG 2024-09-03 06:45:14,474 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [73] queued (34.841 ms) +galaxy.jobs.handler INFO 2024-09-03 06:45:14,476 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:14,479 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 73 +galaxy.jobs DEBUG 2024-09-03 06:45:14,520 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [73] prepared (32.914 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:45:14,521 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:45:14,521 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:45:14,542 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:45:14,563 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/73/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/b/8/0/dataset_b80482de-c2c8-405d-852f-584e16048d2f.dat' solexa '/galaxy/server/database/objects/a/5/f/dataset_a5f73b79-7e2f-4aae-82b6-06fc57063c70.dat' solexa ascii summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:45:14,576 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (73) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/73/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/73/galaxy_73.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:14,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 73 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:45:14,602 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:45:14,602 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:45:14,621 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:14,639 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 73 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:15,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:18,475 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-4ld5q with k8s id: gxy-4ld5q succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:45:18,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 73: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:45:25,537 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 73 finished +galaxy.model.metadata DEBUG 2024-09-03 06:45:25,583 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 73 +galaxy.jobs INFO 2024-09-03 06:45:25,614 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 73 in /galaxy/server/database/jobs_directory/000/73 +galaxy.jobs DEBUG 2024-09-03 06:45:25,685 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 73 executed (127.086 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:25,698 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 73 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:45:26,680 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 74 +tpv.core.entities DEBUG 2024-09-03 06:45:26,702 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:45:26,703 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:45:26,707 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:45:26,719 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:45:26,732 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Working directory for job is: /galaxy/server/database/jobs_directory/000/74 +galaxy.jobs.runners DEBUG 2024-09-03 06:45:26,739 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [74] queued (31.304 ms) +galaxy.jobs.handler INFO 2024-09-03 06:45:26,741 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:26,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 74 +galaxy.jobs DEBUG 2024-09-03 06:45:26,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [74] prepared (75.068 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:45:26,845 [pN:job_handler_0,p:8,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' '74:/galaxy/server/database/objects/8/c/e/dataset_8ce110d2-e9a9-4cb0-8077-ac536d1087f0_files:/galaxy/server/database/objects/8/c/e/dataset_8ce110d2-e9a9-4cb0-8077-ac536d1087f0.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:45:26,854 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:26,868 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 74 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:26,881 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 74 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:27,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:36,631 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-n4mmk with k8s id: gxy-n4mmk succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:45:36,752 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 74: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:45:43,761 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 74 finished +galaxy.model.metadata DEBUG 2024-09-03 06:45:43,809 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 74 +galaxy.jobs INFO 2024-09-03 06:45:43,843 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 74 in /galaxy/server/database/jobs_directory/000/74 +galaxy.jobs DEBUG 2024-09-03 06:45:43,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 74 executed (108.764 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:43,904 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 74 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:45:44,023 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 75 +tpv.core.entities DEBUG 2024-09-03 06:45:44,049 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:45:44,050 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:45:44,054 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:45:44,066 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:45:44,082 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Working directory for job is: /galaxy/server/database/jobs_directory/000/75 +galaxy.jobs.runners DEBUG 2024-09-03 06:45:44,089 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [75] queued (34.815 ms) +galaxy.jobs.handler INFO 2024-09-03 06:45:44,091 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:44,093 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 75 +galaxy.jobs DEBUG 2024-09-03 06:45:44,146 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [75] prepared (44.487 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:45:44,146 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:45:44,146 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:45:44,166 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:45:44,188 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/75/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/8/c/e/dataset_8ce110d2-e9a9-4cb0-8077-ac536d1087f0.dat' solexa '/galaxy/server/database/objects/9/f/8/dataset_9f89d4e0-e487-451c-856a-f1a83d9247f6.dat' solexa decimal summarize_input --fix-id] +galaxy.jobs.runners DEBUG 2024-09-03 06:45:44,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (75) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/75/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/75/galaxy_75.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:44,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 75 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:45:44,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:45:44,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:45:44,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:44,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 75 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:44,654 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:48,719 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-j7pqj with k8s id: gxy-j7pqj succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:45:48,839 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 75: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:45:55,879 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 75 finished +galaxy.model.metadata DEBUG 2024-09-03 06:45:55,918 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 75 +galaxy.jobs INFO 2024-09-03 06:45:55,946 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 75 in /galaxy/server/database/jobs_directory/000/75 +galaxy.jobs DEBUG 2024-09-03 06:45:55,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 75 executed (88.895 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:55,997 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 75 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:45:57,304 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 76 +tpv.core.entities DEBUG 2024-09-03 06:45:57,329 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:45:57,330 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:45:57,334 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:45:57,346 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:45:57,361 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Working directory for job is: /galaxy/server/database/jobs_directory/000/76 +galaxy.jobs.runners DEBUG 2024-09-03 06:45:57,369 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [76] queued (34.746 ms) +galaxy.jobs.handler INFO 2024-09-03 06:45:57,371 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:57,372 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 76 +galaxy.jobs DEBUG 2024-09-03 06:45:57,454 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [76] prepared (75.685 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:45:57,475 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '76:/galaxy/server/database/objects/4/6/2/dataset_46264658-3f70-4f21-8bc4-767b9965501a_files:/galaxy/server/database/objects/4/6/2/dataset_46264658-3f70-4f21-8bc4-767b9965501a.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:45:57,485 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (76) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/76/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/76/galaxy_76.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:57,500 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 76 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:57,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 76 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:45:57,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:06,857 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-cz79v with k8s id: gxy-cz79v succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:46:06,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 76: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:46:13,926 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 76 finished +galaxy.model.metadata DEBUG 2024-09-03 06:46:13,966 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 76 +galaxy.jobs INFO 2024-09-03 06:46:13,995 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 76 in /galaxy/server/database/jobs_directory/000/76 +galaxy.jobs DEBUG 2024-09-03 06:46:14,039 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 76 executed (94.145 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:14,051 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 76 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:46:14,657 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 77 +tpv.core.entities DEBUG 2024-09-03 06:46:14,679 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:46:14,680 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:46:14,683 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:46:14,691 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:46:14,702 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Working directory for job is: /galaxy/server/database/jobs_directory/000/77 +galaxy.jobs.runners DEBUG 2024-09-03 06:46:14,708 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [77] queued (25.432 ms) +galaxy.jobs.handler INFO 2024-09-03 06:46:14,710 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:14,713 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 77 +galaxy.jobs DEBUG 2024-09-03 06:46:14,753 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [77] prepared (34.289 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:46:14,753 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:46:14,753 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:46:14,776 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:46:14,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/77/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/4/6/2/dataset_46264658-3f70-4f21-8bc4-767b9965501a.dat' sanger.gz '/galaxy/server/database/objects/0/2/c/dataset_02ce87b3-3454-4ad3-83df-7d3fd4f7d3f5.dat' sanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2024-09-03 06:46:14,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (77) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/77/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/77/galaxy_77.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:14,830 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 77 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:46:14,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:46:14,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:46:14,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:14,871 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 77 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:15,881 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:18,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-7l5xz failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:18,933 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:18,954 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-7l5xz. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:18,963 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 77 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-09-03 06:46:18,981 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-09-03-06-11-1/jobs/gxy-7l5xz + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-7l5xz": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:18,990 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:18,996 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (77/gxy-7l5xz) tool_stdout: Groomed 2 sanger.gz reads into sanger reads. +Based upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2 +Input ASCII range: '!'(33) - '~'(126) +Input decimal range: 0 - 93 + +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:18,996 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (77/gxy-7l5xz) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:18,996 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (77/gxy-7l5xz) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:18,996 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (77/gxy-7l5xz) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-7l5xz. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:18,996 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Attempting to stop job 77 (gxy-7l5xz) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:19,002 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Found job with id gxy-7l5xz to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:19,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 77 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:19,049 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (77/gxy-7l5xz) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-09-03 06:46:20,800 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 78 +tpv.core.entities DEBUG 2024-09-03 06:46:20,824 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:46:20,824 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:46:20,827 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:46:20,836 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:46:20,846 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Working directory for job is: /galaxy/server/database/jobs_directory/000/78 +galaxy.jobs.runners DEBUG 2024-09-03 06:46:20,852 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [78] queued (24.869 ms) +galaxy.jobs.handler INFO 2024-09-03 06:46:20,855 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:20,856 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 78 +galaxy.jobs DEBUG 2024-09-03 06:46:20,928 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [78] prepared (64.587 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:46:20,945 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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' '78:/galaxy/server/database/objects/1/4/c/dataset_14c0a2e7-49a4-4303-a1d3-6e5860e79af0_files:/galaxy/server/database/objects/1/4/c/dataset_14c0a2e7-49a4-4303-a1d3-6e5860e79af0.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:46:20,953 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (78) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/78/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/78/galaxy_78.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:20,966 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 78 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:20,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 78 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:22,006 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:30,126 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-fwx76 with k8s id: gxy-fwx76 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:46:30,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 78: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:46:37,323 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 78 finished +galaxy.model.metadata DEBUG 2024-09-03 06:46:37,365 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 78 +galaxy.jobs INFO 2024-09-03 06:46:37,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 78 in /galaxy/server/database/jobs_directory/000/78 +galaxy.jobs DEBUG 2024-09-03 06:46:37,444 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 78 executed (100.488 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:37,455 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 78 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:46:38,129 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 79 +tpv.core.entities DEBUG 2024-09-03 06:46:38,155 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/fastq_groomer/fastq_groomer/.*, abstract=False, cores=1, mem=7.6, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:46:38,156 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:46:38,160 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:46:38,174 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:46:38,188 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Working directory for job is: /galaxy/server/database/jobs_directory/000/79 +galaxy.jobs.runners DEBUG 2024-09-03 06:46:38,197 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [79] queued (37.081 ms) +galaxy.jobs.handler INFO 2024-09-03 06:46:38,201 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:38,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 79 +galaxy.jobs DEBUG 2024-09-03 06:46:38,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [79] prepared (39.956 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:46:38,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:46:38,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:46:38,270 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:46:38,293 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/79/tool_script.sh] for tool command [gx-fastq-groomer '/galaxy/server/database/objects/1/4/c/dataset_14c0a2e7-49a4-4303-a1d3-6e5860e79af0.dat' cssanger.bz2 '/galaxy/server/database/objects/d/5/e/dataset_d5e7c3d0-28dd-4b0d-b0d5-8e1a95a4b850.dat' cssanger ascii summarize_input] +galaxy.jobs.runners DEBUG 2024-09-03 06:46:38,306 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:38,323 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 79 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:46:38,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:46:38,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5: galaxy_sequence_utils:1.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:46:38,349 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/galaxy_sequence_utils:1.1.5--pyh7e72e81_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:38,370 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 79 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:39,154 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:42,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-wgn9p with k8s id: gxy-wgn9p succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:46:42,332 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 79: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:46:49,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 79 finished +galaxy.model.metadata DEBUG 2024-09-03 06:46:49,264 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 79 +galaxy.jobs INFO 2024-09-03 06:46:49,297 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 79 in /galaxy/server/database/jobs_directory/000/79 +galaxy.jobs DEBUG 2024-09-03 06:46:49,339 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 79 executed (97.478 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:49,351 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 79 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:46:52,428 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 81, 80 +tpv.core.entities DEBUG 2024-09-03 06:46:52,453 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:46:52,453 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:46:52,457 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:46:52,467 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:46:52,480 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Working directory for job is: /galaxy/server/database/jobs_directory/000/80 +galaxy.jobs.runners DEBUG 2024-09-03 06:46:52,487 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [80] queued (30.354 ms) +galaxy.jobs.handler INFO 2024-09-03 06:46:52,490 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:52,493 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 80 +tpv.core.entities DEBUG 2024-09-03 06:46:52,501 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:46:52,502 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:46:52,506 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:46:52,516 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:46:52,538 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Working directory for job is: /galaxy/server/database/jobs_directory/000/81 +galaxy.jobs.runners DEBUG 2024-09-03 06:46:52,544 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [81] queued (37.980 ms) +galaxy.jobs.handler INFO 2024-09-03 06:46:52,547 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:52,550 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 81 +galaxy.jobs DEBUG 2024-09-03 06:46:52,592 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [80] prepared (87.214 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:46:52,610 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/80/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/80/registry.xml' '/galaxy/server/database/jobs_directory/000/80/upload_params.json' '80:/galaxy/server/database/objects/0/d/c/dataset_0dcd2410-b7e5-4fc0-a519-11cb579b069e_files:/galaxy/server/database/objects/0/d/c/dataset_0dcd2410-b7e5-4fc0-a519-11cb579b069e.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:46:52,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (80) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/80/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/80/galaxy_80.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-09-03 06:46:52,633 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [81] prepared (70.340 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:52,636 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 80 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:52,653 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 80 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-09-03 06:46:52,656 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/81/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/81/registry.xml' '/galaxy/server/database/jobs_directory/000/81/upload_params.json' '81:/galaxy/server/database/objects/d/5/f/dataset_d5f8bb69-e1d0-41c6-bb90-a1915f73f891_files:/galaxy/server/database/objects/d/5/f/dataset_d5f8bb69-e1d0-41c6-bb90-a1915f73f891.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:46:52,665 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (81) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/81/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/81/galaxy_81.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:52,678 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 81 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:52,690 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 81 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:53,322 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:53,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-09-03 06:46:53,551 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 82 +tpv.core.entities DEBUG 2024-09-03 06:46:53,574 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:46:53,574 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:46:53,577 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:46:53,587 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:46:53,602 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Working directory for job is: /galaxy/server/database/jobs_directory/000/82 +galaxy.jobs.runners DEBUG 2024-09-03 06:46:53,609 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [82] queued (32.356 ms) +galaxy.jobs.handler INFO 2024-09-03 06:46:53,611 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:53,614 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 82 +galaxy.jobs DEBUG 2024-09-03 06:46:53,693 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [82] prepared (72.521 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:46:53,713 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/82/tool_script.sh] for tool command [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' '82:/galaxy/server/database/objects/c/2/d/dataset_c2d07c4b-f9da-4717-9c08-b0aa1effd6b5_files:/galaxy/server/database/objects/c/2/d/dataset_c2d07c4b-f9da-4717-9c08-b0aa1effd6b5.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:46:53,724 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (82) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/82/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/82/galaxy_82.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:53,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 82 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:53,750 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 82 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:46:54,465 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:03,729 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-7mf6z with k8s id: gxy-7mf6z succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:03,741 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-98sds with k8s id: gxy-98sds succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:03,756 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-599wm with k8s id: gxy-599wm succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:47:03,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 81: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:47:03,900 [pN:job_handler_0,p:8,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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:47:03,934 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 82: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:47:14,994 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 81 finished +galaxy.model.metadata DEBUG 2024-09-03 06:47:15,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 81 +galaxy.jobs.runners DEBUG 2024-09-03 06:47:15,084 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 80 finished +galaxy.jobs INFO 2024-09-03 06:47:15,113 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 81 in /galaxy/server/database/jobs_directory/000/81 +galaxy.model.metadata DEBUG 2024-09-03 06:47:15,136 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 80 +galaxy.jobs INFO 2024-09-03 06:47:15,171 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 80 in /galaxy/server/database/jobs_directory/000/80 +galaxy.jobs.runners DEBUG 2024-09-03 06:47:15,178 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 82 finished +galaxy.jobs DEBUG 2024-09-03 06:47:15,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 81 executed (176.368 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:15,211 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 81 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.model.metadata DEBUG 2024-09-03 06:47:15,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 82 +galaxy.jobs DEBUG 2024-09-03 06:47:15,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 80 executed (136.450 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:15,259 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 80 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs INFO 2024-09-03 06:47:15,264 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 82 in /galaxy/server/database/jobs_directory/000/82 +galaxy.jobs DEBUG 2024-09-03 06:47:15,327 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 82 executed (125.731 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:15,347 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 82 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:47:16,305 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 83 +tpv.core.entities DEBUG 2024-09-03 06:47:16,336 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:47:16,337 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:47:16,340 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:47:16,350 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:47:16,373 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Working directory for job is: /galaxy/server/database/jobs_directory/000/83 +galaxy.jobs.runners DEBUG 2024-09-03 06:47:16,381 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [83] queued (40.801 ms) +galaxy.jobs.handler INFO 2024-09-03 06:47:16,383 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:16,386 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 83 +galaxy.jobs DEBUG 2024-09-03 06:47:16,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [83] prepared (52.503 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:47:16,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:47:16,447 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1: mulled-v2-c5f548bbd369f6c53d1c17c3956a106c0348c719:a35fc6d6deba8537e98b27e27bb305fb3def739c +galaxy.tool_util.deps.containers INFO 2024-09-03 06:47:16,638 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-c5f548bbd369f6c53d1c17c3956a106c0348c719:a35fc6d6deba8537e98b27e27bb305fb3def739c-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:47:16,657 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/83/tool_script.sh] for tool command [ln -s /galaxy/server/database/objects/d/5/f/dataset_d5f8bb69-e1d0-41c6-bb90-a1915f73f891.dat reference.fa && ln -s /galaxy/server/database/objects/c/2/d/dataset_c2d07c4b-f9da-4717-9c08-b0aa1effd6b5.dat query.fa && mummerplot -b '20' -s 'small' -terminal png -title 'Title' '/galaxy/server/database/objects/0/d/c/dataset_0dcd2410-b7e5-4fc0-a519-11cb579b069e.dat' && gnuplot < out.gp] +galaxy.jobs.runners DEBUG 2024-09-03 06:47:16,686 [pN:job_handler_0,p:8,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; +if [ -f "/galaxy/server/database/jobs_directory/000/83/working/out.gp" -a -f "/galaxy/server/database/objects/8/6/e/dataset_86e00b30-a643-437e-8486-f0c0522d9ffe.dat" ] ; then cp "/galaxy/server/database/jobs_directory/000/83/working/out.gp" "/galaxy/server/database/objects/8/6/e/dataset_86e00b30-a643-437e-8486-f0c0522d9ffe.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/83/working/out.fplot" -a -f "/galaxy/server/database/objects/3/b/9/dataset_3b9b5c07-f5e2-4f0e-ab32-90938f11c222.dat" ] ; then cp "/galaxy/server/database/jobs_directory/000/83/working/out.fplot" "/galaxy/server/database/objects/3/b/9/dataset_3b9b5c07-f5e2-4f0e-ab32-90938f11c222.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/83/working/out.rplot" -a -f "/galaxy/server/database/objects/e/1/a/dataset_e1ae18a3-45d4-4707-8014-66a876589ab0.dat" ] ; then cp "/galaxy/server/database/jobs_directory/000/83/working/out.rplot" "/galaxy/server/database/objects/e/1/a/dataset_e1ae18a3-45d4-4707-8014-66a876589ab0.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/83/working/out.hplot" -a -f "/galaxy/server/database/objects/e/9/1/dataset_e913752d-b895-4930-8968-63bdcc71d915.dat" ] ; then cp "/galaxy/server/database/jobs_directory/000/83/working/out.hplot" "/galaxy/server/database/objects/e/9/1/dataset_e913752d-b895-4930-8968-63bdcc71d915.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/83/working/out.png" -a -f "/galaxy/server/database/objects/0/c/6/dataset_0c697ffa-3c9e-4080-9039-c62257f0e4e9.dat" ] ; then cp "/galaxy/server/database/jobs_directory/000/83/working/out.png" "/galaxy/server/database/objects/0/c/6/dataset_0c697ffa-3c9e-4080-9039-c62257f0e4e9.dat" ; fi; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:16,699 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 83 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:47:16,699 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:47:16,700 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1: mulled-v2-c5f548bbd369f6c53d1c17c3956a106c0348c719:a35fc6d6deba8537e98b27e27bb305fb3def739c +galaxy.tool_util.deps.containers INFO 2024-09-03 06:47:16,716 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-c5f548bbd369f6c53d1c17c3956a106c0348c719:a35fc6d6deba8537e98b27e27bb305fb3def739c-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:16,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 83 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:17,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:41,186 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-z6ksb with k8s id: gxy-z6ksb succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:47:41,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 83: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:47:48,582 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 83 finished +galaxy.model.metadata DEBUG 2024-09-03 06:47:48,630 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 83 +galaxy.model.metadata DEBUG 2024-09-03 06:47:48,639 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 84 +galaxy.model.metadata DEBUG 2024-09-03 06:47:48,649 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 85 +galaxy.model.metadata DEBUG 2024-09-03 06:47:48,659 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 86 +galaxy.model.metadata DEBUG 2024-09-03 06:47:48,669 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 87 +galaxy.jobs INFO 2024-09-03 06:47:48,714 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 83 in /galaxy/server/database/jobs_directory/000/83 +galaxy.jobs DEBUG 2024-09-03 06:47:48,772 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 83 executed (169.681 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:48,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 83 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:47:52,980 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 84 +tpv.core.entities DEBUG 2024-09-03 06:47:53,010 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:47:53,010 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:47:53,015 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:47:53,028 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:47:53,045 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Working directory for job is: /galaxy/server/database/jobs_directory/000/84 +galaxy.jobs.runners DEBUG 2024-09-03 06:47:53,053 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [84] queued (37.399 ms) +galaxy.jobs.handler INFO 2024-09-03 06:47:53,056 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:53,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 84 +galaxy.jobs DEBUG 2024-09-03 06:47:53,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [84] prepared (79.575 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:47:53,164 [pN:job_handler_0,p:8,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' '88:/galaxy/server/database/objects/d/2/f/dataset_d2fec9b0-b293-4776-92c2-29d1d63f9246_files:/galaxy/server/database/objects/d/2/f/dataset_d2fec9b0-b293-4776-92c2-29d1d63f9246.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:47:53,175 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:53,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 84 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:53,210 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 84 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:47:54,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:48:02,320 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-jlm6m with k8s id: gxy-jlm6m succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:48:02,458 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 84: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:48:09,584 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 84 finished +galaxy.model.metadata DEBUG 2024-09-03 06:48:09,626 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 88 +galaxy.jobs INFO 2024-09-03 06:48:09,653 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 84 in /galaxy/server/database/jobs_directory/000/84 +galaxy.jobs DEBUG 2024-09-03 06:48:09,696 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 84 executed (92.326 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:48:09,707 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 84 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:48:10,338 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 85 +tpv.core.entities DEBUG 2024-09-03 06:48:10,367 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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_qualpos/poretools_qualpos/.*, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:48:10,367 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:48:10,371 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:48:10,382 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:48:10,397 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Working directory for job is: /galaxy/server/database/jobs_directory/000/85 +galaxy.jobs.runners DEBUG 2024-09-03 06:48:10,404 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [85] queued (32.843 ms) +galaxy.jobs.handler INFO 2024-09-03 06:48:10,407 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:48:10,409 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 85 +galaxy.jobs DEBUG 2024-09-03 06:48:10,465 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [85] prepared (45.956 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:48:10,465 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:48:10,465 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:48:10,758 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:48:10,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/85/tool_script.sh] for tool command [export MPLBACKEND="agg" && poretools qualpos '/galaxy/server/database/objects/d/2/f/dataset_d2fec9b0-b293-4776-92c2-29d1d63f9246.dat' --saveas qualpos.png --min-length 0 --max-length 1000000000 --bin-width 1000 && mv qualpos.png '/galaxy/server/database/objects/7/b/6/dataset_7b65c684-a375-4ad2-add9-2d06a1137cf8.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:48:10,805 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:48:10,823 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 85 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:48:10,829 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:48:10,830 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:48:10,849 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:48:10,869 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 85 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:48:11,345 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:48:37,661 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-cv6ms with k8s id: gxy-cv6ms succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:48:37,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 85: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:48:44,725 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 85 finished +galaxy.model.metadata DEBUG 2024-09-03 06:48:44,769 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 89 +galaxy.util WARNING 2024-09-03 06:48:44,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/7/b/6/dataset_7b65c684-a375-4ad2-add9-2d06a1137cf8.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/7/b/6/dataset_7b65c684-a375-4ad2-add9-2d06a1137cf8.dat' +galaxy.jobs INFO 2024-09-03 06:48:44,801 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 85 in /galaxy/server/database/jobs_directory/000/85 +galaxy.jobs DEBUG 2024-09-03 06:48:44,848 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 85 executed (102.220 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:48:44,860 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 85 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:48:47,009 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 86 +tpv.core.entities DEBUG 2024-09-03 06:48:47,034 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:48:47,035 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:48:47,038 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:48:47,050 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:48:47,065 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Working directory for job is: /galaxy/server/database/jobs_directory/000/86 +galaxy.jobs.runners DEBUG 2024-09-03 06:48:47,072 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [86] queued (33.467 ms) +galaxy.jobs.handler INFO 2024-09-03 06:48:47,074 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:48:47,076 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 86 +galaxy.jobs DEBUG 2024-09-03 06:48:47,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [86] prepared (72.497 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:48:47,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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' '90:/galaxy/server/database/objects/8/0/2/dataset_80265725-3d70-4928-be93-db0fceda3fc8_files:/galaxy/server/database/objects/8/0/2/dataset_80265725-3d70-4928-be93-db0fceda3fc8.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:48:47,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (86) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/86/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/86/galaxy_86.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:48:47,199 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 86 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:48:47,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 86 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:48:47,690 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:48:56,830 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-6xs7g with k8s id: gxy-6xs7g succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:48:56,948 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 86: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:49:04,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 86 finished +galaxy.model.metadata DEBUG 2024-09-03 06:49:04,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 90 +galaxy.jobs INFO 2024-09-03 06:49:04,209 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 86 in /galaxy/server/database/jobs_directory/000/86 +galaxy.jobs DEBUG 2024-09-03 06:49:04,265 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 86 executed (112.906 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:04,277 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 86 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:49:05,367 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 87 +tpv.core.entities DEBUG 2024-09-03 06:49:05,390 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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_qualpos/poretools_qualpos/.*, 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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:49:05,391 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:49:05,394 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:49:05,402 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:49:05,415 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Working directory for job is: /galaxy/server/database/jobs_directory/000/87 +galaxy.jobs.runners DEBUG 2024-09-03 06:49:05,423 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [87] queued (29.455 ms) +galaxy.jobs.handler INFO 2024-09-03 06:49:05,426 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:05,429 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 87 +galaxy.jobs DEBUG 2024-09-03 06:49:05,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [87] prepared (38.145 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:49:05,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:49:05,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:49:05,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:49:05,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/87/tool_script.sh] for tool command [export MPLBACKEND="agg" && poretools qualpos '/galaxy/server/database/objects/8/0/2/dataset_80265725-3d70-4928-be93-db0fceda3fc8.dat' --saveas qualpos.pdf --min-length 0 --max-length 1000000000 --bin-width 1000 && mv qualpos.pdf '/galaxy/server/database/objects/4/9/a/dataset_49aba569-df85-4140-8d2e-73762a5d0fb5.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:49:05,527 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (87) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/87/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/87/galaxy_87.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:05,544 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 87 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:49:05,550 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:49:05,550 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:49:05,568 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:05,591 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 87 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:05,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:11,956 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-fh5d4 with k8s id: gxy-fh5d4 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:49:12,091 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 87: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:49:19,247 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 87 finished +galaxy.model.metadata DEBUG 2024-09-03 06:49:19,285 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 91 +galaxy.util WARNING 2024-09-03 06:49:19,289 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/4/9/a/dataset_49aba569-df85-4140-8d2e-73762a5d0fb5.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/a/dataset_49aba569-df85-4140-8d2e-73762a5d0fb5.dat' +galaxy.jobs INFO 2024-09-03 06:49:19,312 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 87 in /galaxy/server/database/jobs_directory/000/87 +galaxy.jobs DEBUG 2024-09-03 06:49:19,351 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 87 executed (85.617 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:19,363 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 87 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:49:21,684 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 89, 88 +tpv.core.entities DEBUG 2024-09-03 06:49:21,708 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:49:21,709 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:49:21,712 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:49:21,723 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:49:21,738 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Working directory for job is: /galaxy/server/database/jobs_directory/000/88 +galaxy.jobs.runners DEBUG 2024-09-03 06:49:21,744 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [88] queued (31.367 ms) +galaxy.jobs.handler INFO 2024-09-03 06:49:21,746 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:21,750 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 88 +tpv.core.entities DEBUG 2024-09-03 06:49:21,759 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:49:21,759 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:49:21,764 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:49:21,779 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:49:21,808 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Working directory for job is: /galaxy/server/database/jobs_directory/000/89 +galaxy.jobs.runners DEBUG 2024-09-03 06:49:21,816 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [89] queued (51.587 ms) +galaxy.jobs.handler INFO 2024-09-03 06:49:21,819 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:21,823 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 89 +galaxy.jobs DEBUG 2024-09-03 06:49:21,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [88] prepared (101.561 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:49:21,896 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/88/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/88/registry.xml' '/galaxy/server/database/jobs_directory/000/88/upload_params.json' '92:/galaxy/server/database/objects/2/0/8/dataset_20841d69-45c2-45c8-9f0b-e233b86dd4d1_files:/galaxy/server/database/objects/2/0/8/dataset_20841d69-45c2-45c8-9f0b-e233b86dd4d1.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:49:21,908 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (88) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/88/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/88/galaxy_88.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-09-03 06:49:21,921 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [89] prepared (86.255 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:21,924 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 88 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:21,938 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 88 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-09-03 06:49:21,945 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/89/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/89/registry.xml' '/galaxy/server/database/jobs_directory/000/89/upload_params.json' '93:/galaxy/server/database/objects/b/9/9/dataset_b99f2814-b84f-4a2a-9f92-60b441ebd20a_files:/galaxy/server/database/objects/b/9/9/dataset_b99f2814-b84f-4a2a-9f92-60b441ebd20a.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:49:21,953 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (89) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/89/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/89/galaxy_89.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:21,967 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 89 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:21,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 89 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:49:22,824 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 90 +tpv.core.entities DEBUG 2024-09-03 06:49:22,855 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:49:22,856 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:49:22,860 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:49:22,872 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:49:22,888 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Working directory for job is: /galaxy/server/database/jobs_directory/000/90 +galaxy.jobs.runners DEBUG 2024-09-03 06:49:22,895 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [90] queued (34.783 ms) +galaxy.jobs.handler INFO 2024-09-03 06:49:22,898 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:22,900 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 90 +galaxy.jobs DEBUG 2024-09-03 06:49:22,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [90] prepared (76.427 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:49:23,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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' '94:/galaxy/server/database/objects/1/9/c/dataset_19c1f94b-8f2b-4657-b321-f16c7e9248e3_files:/galaxy/server/database/objects/1/9/c/dataset_19c1f94b-8f2b-4657-b321-f16c7e9248e3.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:49:23,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:23,043 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:23,053 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 90 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:23,083 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 90 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:23,180 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:24,241 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:31,453 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-rskd8 with k8s id: gxy-rskd8 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:31,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-pvmgx with k8s id: gxy-pvmgx succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:49:31,590 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 89: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:49:31,591 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:32,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-w9c5v with k8s id: gxy-w9c5v succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:49:32,616 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 90: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:49:42,366 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 88 finished +galaxy.model.metadata DEBUG 2024-09-03 06:49:42,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 92 +galaxy.jobs INFO 2024-09-03 06:49:42,471 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 88 in /galaxy/server/database/jobs_directory/000/88 +galaxy.jobs.runners DEBUG 2024-09-03 06:49:42,503 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 89 finished +galaxy.jobs DEBUG 2024-09-03 06:49:42,531 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 88 executed (143.434 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:42,544 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 88 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.model.metadata DEBUG 2024-09-03 06:49:42,556 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 93 +galaxy.jobs INFO 2024-09-03 06:49:42,587 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 89 in /galaxy/server/database/jobs_directory/000/89 +galaxy.jobs DEBUG 2024-09-03 06:49:42,634 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 89 executed (112.855 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:42,646 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 89 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-09-03 06:49:43,384 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 90 finished +galaxy.model.metadata DEBUG 2024-09-03 06:49:43,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 94 +galaxy.jobs INFO 2024-09-03 06:49:43,453 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 90 in /galaxy/server/database/jobs_directory/000/90 +galaxy.jobs DEBUG 2024-09-03 06:49:43,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 90 executed (93.828 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:43,508 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 90 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:49:44,342 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 91 +tpv.core.entities DEBUG 2024-09-03 06:49:44,373 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:49:44,374 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:49:44,377 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:49:44,387 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:49:44,400 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Working directory for job is: /galaxy/server/database/jobs_directory/000/91 +galaxy.jobs.runners DEBUG 2024-09-03 06:49:44,410 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [91] queued (32.952 ms) +galaxy.jobs.handler INFO 2024-09-03 06:49:44,413 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:44,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 91 +galaxy.jobs DEBUG 2024-09-03 06:49:44,490 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [91] prepared (67.180 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:49:44,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:49:44,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:49:44,665 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:49:44,688 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/91/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/2/0/8/dataset_20841d69-45c2-45c8-9f0b-e233b86dd4d1.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . --batch '/galaxy/server/database/jobs_directory/000/91/configs/tmplixzjma7' --umi && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi] +galaxy.jobs.runners DEBUG 2024-09-03 06:49:44,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (91) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/91/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/91/galaxy_91.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:44,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 91 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:49:44,710 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:49:44,710 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:49:44,728 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:44,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 91 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:45,590 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:51,678 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-dfq4f with k8s id: gxy-dfq4f succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:49:51,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 91: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:49:58,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 91 finished +galaxy.model.metadata DEBUG 2024-09-03 06:49:58,983 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 95 +galaxy.jobs INFO 2024-09-03 06:49:59,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 91 in /galaxy/server/database/jobs_directory/000/91 +galaxy.jobs DEBUG 2024-09-03 06:49:59,086 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 91 executed (224.756 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:49:59,097 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 91 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:50:06,790 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 94, 92, 93 +tpv.core.entities DEBUG 2024-09-03 06:50:06,817 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:50:06,817 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:50:06,820 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:50:06,830 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:50:06,844 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Working directory for job is: /galaxy/server/database/jobs_directory/000/92 +galaxy.jobs.runners DEBUG 2024-09-03 06:50:06,852 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [92] queued (31.905 ms) +galaxy.jobs.handler INFO 2024-09-03 06:50:06,855 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:06,859 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 92 +tpv.core.entities DEBUG 2024-09-03 06:50:06,869 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:50:06,869 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:50:06,874 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:50:06,890 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:50:06,924 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Working directory for job is: /galaxy/server/database/jobs_directory/000/93 +galaxy.jobs.runners DEBUG 2024-09-03 06:50:06,932 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [93] queued (57.373 ms) +galaxy.jobs.handler INFO 2024-09-03 06:50:06,936 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:06,941 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 93 +tpv.core.entities DEBUG 2024-09-03 06:50:06,954 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:50:06,954 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:50:06,957 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:50:06,971 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:50:06,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [92] prepared (113.894 ms) +galaxy.jobs DEBUG 2024-09-03 06:50:07,010 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Working directory for job is: /galaxy/server/database/jobs_directory/000/94 +galaxy.jobs.runners DEBUG 2024-09-03 06:50:07,019 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [94] queued (61.423 ms) +galaxy.jobs.handler INFO 2024-09-03 06:50:07,023 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:07,026 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 94 +galaxy.jobs.command_factory INFO 2024-09-03 06:50:07,027 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/92/tool_script.sh] for tool command [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' '99:/galaxy/server/database/objects/d/b/0/dataset_db05ff2a-ca84-44e4-a884-88de30814045_files:/galaxy/server/database/objects/d/b/0/dataset_db05ff2a-ca84-44e4-a884-88de30814045.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:50:07,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (92) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/92/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/92/galaxy_92.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:07,057 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 92 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-09-03 06:50:07,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [93] prepared (110.249 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:07,088 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 92 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-09-03 06:50:07,106 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/93/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/93/registry.xml' '/galaxy/server/database/jobs_directory/000/93/upload_params.json' '100:/galaxy/server/database/objects/f/5/b/dataset_f5b5a17e-5ca4-48d8-a4e5-448142357b8e_files:/galaxy/server/database/objects/f/5/b/dataset_f5b5a17e-5ca4-48d8-a4e5-448142357b8e.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:50:07,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (93) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/93/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/93/galaxy_93.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-09-03 06:50:07,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [94] prepared (109.761 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:07,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 93 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-09-03 06:50:07,179 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/94/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/94/registry.xml' '/galaxy/server/database/jobs_directory/000/94/upload_params.json' '101:/galaxy/server/database/objects/3/5/1/dataset_351c7ba6-9bc9-4213-80e3-6bf7d2d5acfd_files:/galaxy/server/database/objects/3/5/1/dataset_351c7ba6-9bc9-4213-80e3-6bf7d2d5acfd.dat'] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:07,190 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 93 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-09-03 06:50:07,191 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (94) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/94/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/94/galaxy_94.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:07,209 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 94 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:07,223 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 94 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:07,930 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:08,040 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:08,132 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:17,409 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-52clk with k8s id: gxy-52clk succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:17,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-6wtk9 with k8s id: gxy-6wtk9 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:17,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-c5b86 with k8s id: gxy-c5b86 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:50:17,568 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 92: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:50:17,589 [pN:job_handler_0,p:8,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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:50:17,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 94: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:50:28,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 93 finished +galaxy.model.metadata DEBUG 2024-09-03 06:50:28,925 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 100 +galaxy.jobs.runners DEBUG 2024-09-03 06:50:28,974 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 94 finished +galaxy.jobs INFO 2024-09-03 06:50:28,984 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 93 in /galaxy/server/database/jobs_directory/000/93 +galaxy.jobs.runners DEBUG 2024-09-03 06:50:29,003 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 92 finished +galaxy.model.metadata DEBUG 2024-09-03 06:50:29,020 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 101 +galaxy.model.metadata DEBUG 2024-09-03 06:50:29,059 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 99 +galaxy.jobs INFO 2024-09-03 06:50:29,061 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 94 in /galaxy/server/database/jobs_directory/000/94 +galaxy.jobs DEBUG 2024-09-03 06:50:29,078 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 93 executed (171.533 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:29,095 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 93 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs INFO 2024-09-03 06:50:29,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 92 in /galaxy/server/database/jobs_directory/000/92 +galaxy.jobs DEBUG 2024-09-03 06:50:29,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 94 executed (142.784 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:29,152 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 94 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-09-03 06:50:29,165 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 92 executed (138.535 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:29,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 92 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:50:29,671 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 95 +tpv.core.entities DEBUG 2024-09-03 06:50:29,701 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:50:29,702 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:50:29,707 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:50:29,719 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:50:29,732 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Working directory for job is: /galaxy/server/database/jobs_directory/000/95 +galaxy.jobs.runners DEBUG 2024-09-03 06:50:29,740 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [95] queued (32.619 ms) +galaxy.jobs.handler INFO 2024-09-03 06:50:29,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:29,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 95 +galaxy.jobs DEBUG 2024-09-03 06:50:29,835 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [95] prepared (82.166 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:50:29,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:50:29,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:50:29,855 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:50:29,874 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/95/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/d/b/0/dataset_db05ff2a-ca84-44e4-a884-88de30814045.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . '/galaxy/server/database/objects/f/5/b/dataset_f5b5a17e-5ca4-48d8-a4e5-448142357b8e.dat' '/galaxy/server/database/objects/3/5/1/dataset_351c7ba6-9bc9-4213-80e3-6bf7d2d5acfd.dat' && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi] +galaxy.jobs.runners DEBUG 2024-09-03 06:50:29,884 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (95) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/95/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/95/galaxy_95.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:29,898 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 95 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:50:29,899 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:50:29,899 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:50:29,920 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:29,942 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 95 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:30,498 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:34,564 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-5dpdj with k8s id: gxy-5dpdj succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:50:34,704 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 95: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:50:41,776 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 95 finished +galaxy.model.metadata DEBUG 2024-09-03 06:50:42,027 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 102 +galaxy.jobs INFO 2024-09-03 06:50:42,102 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 95 in /galaxy/server/database/jobs_directory/000/95 +galaxy.jobs DEBUG 2024-09-03 06:50:42,126 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 95 executed (327.066 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:42,141 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 95 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:50:44,001 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 97, 96 +tpv.core.entities DEBUG 2024-09-03 06:50:44,023 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:50:44,023 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:50:44,027 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:50:44,038 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:50:44,050 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Working directory for job is: /galaxy/server/database/jobs_directory/000/96 +galaxy.jobs.runners DEBUG 2024-09-03 06:50:44,058 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [96] queued (30.356 ms) +galaxy.jobs.handler INFO 2024-09-03 06:50:44,060 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:44,062 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 96 +tpv.core.entities DEBUG 2024-09-03 06:50:44,069 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:50:44,070 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:50:44,074 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:50:44,085 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:50:44,108 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Working directory for job is: /galaxy/server/database/jobs_directory/000/97 +galaxy.jobs.runners DEBUG 2024-09-03 06:50:44,116 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [97] queued (41.968 ms) +galaxy.jobs.handler INFO 2024-09-03 06:50:44,118 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:44,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 97 +galaxy.jobs DEBUG 2024-09-03 06:50:44,173 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [96] prepared (100.807 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:50:44,198 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/96/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/96/registry.xml' '/galaxy/server/database/jobs_directory/000/96/upload_params.json' '108:/galaxy/server/database/objects/c/e/e/dataset_cee4f51e-5244-472f-ab51-5622f9174f53_files:/galaxy/server/database/objects/c/e/e/dataset_cee4f51e-5244-472f-ab51-5622f9174f53.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:50:44,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (96) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/96/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/96/galaxy_96.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-09-03 06:50:44,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [97] prepared (90.243 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:44,229 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 96 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:44,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 96 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-09-03 06:50:44,253 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/97/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/97/registry.xml' '/galaxy/server/database/jobs_directory/000/97/upload_params.json' '109:/galaxy/server/database/objects/3/b/3/dataset_3b3b7702-1a14-43f1-a1e4-2c60dee8c3c9_files:/galaxy/server/database/objects/3/b/3/dataset_3b3b7702-1a14-43f1-a1e4-2c60dee8c3c9.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:50:44,264 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (97) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/97/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/97/galaxy_97.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:44,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 97 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:44,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 97 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:44,591 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:44,632 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:53,865 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-g5pdv with k8s id: gxy-g5pdv succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:50:53,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-pklm8 with k8s id: gxy-pklm8 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:50:54,016 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 96: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:50:54,028 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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 2024-09-03 06:51:01,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 97 finished +galaxy.jobs.runners DEBUG 2024-09-03 06:51:01,576 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 96 finished +galaxy.model.metadata DEBUG 2024-09-03 06:51:01,583 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 109 +galaxy.jobs INFO 2024-09-03 06:51:01,621 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 97 in /galaxy/server/database/jobs_directory/000/97 +galaxy.model.metadata DEBUG 2024-09-03 06:51:01,628 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 108 +galaxy.jobs INFO 2024-09-03 06:51:01,658 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 96 in /galaxy/server/database/jobs_directory/000/96 +galaxy.jobs DEBUG 2024-09-03 06:51:01,679 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 97 executed (124.873 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:01,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 97 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-09-03 06:51:01,719 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 96 executed (117.707 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:01,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 96 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:51:02,471 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 98 +tpv.core.entities DEBUG 2024-09-03 06:51:02,501 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:51:02,501 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:51:02,506 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:51:02,515 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:51:02,528 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Working directory for job is: /galaxy/server/database/jobs_directory/000/98 +galaxy.jobs.runners DEBUG 2024-09-03 06:51:02,536 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [98] queued (30.548 ms) +galaxy.jobs.handler INFO 2024-09-03 06:51:02,538 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:02,541 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 98 +galaxy.jobs DEBUG 2024-09-03 06:51:02,607 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [98] prepared (56.747 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:51:02,607 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:51:02,608 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:51:02,629 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:51:02,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/98/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/c/e/e/dataset_cee4f51e-5244-472f-ab51-5622f9174f53.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . --single --fragment-length 200 --sd 20 '/galaxy/server/database/objects/3/b/3/dataset_3b3b7702-1a14-43f1-a1e4-2c60dee8c3c9.dat' && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi] +galaxy.jobs.runners DEBUG 2024-09-03 06:51:02,659 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (98) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/98/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/98/galaxy_98.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:02,673 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 98 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:51:02,673 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:51:02,673 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:51:02,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:02,707 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 98 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:02,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:07,145 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-snxts with k8s id: gxy-snxts succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:51:07,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 98: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:51:14,400 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 98 finished +galaxy.model.metadata DEBUG 2024-09-03 06:51:14,647 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 110 +galaxy.jobs INFO 2024-09-03 06:51:14,717 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 98 in /galaxy/server/database/jobs_directory/000/98 +galaxy.jobs DEBUG 2024-09-03 06:51:14,738 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 98 executed (319.841 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:14,752 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 98 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:51:16,281 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 99 +tpv.core.entities DEBUG 2024-09-03 06:51:16,303 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:51:16,303 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:51:16,307 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:51:16,320 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:51:16,334 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Working directory for job is: /galaxy/server/database/jobs_directory/000/99 +galaxy.jobs.runners DEBUG 2024-09-03 06:51:16,341 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [99] queued (33.307 ms) +galaxy.jobs.handler INFO 2024-09-03 06:51:16,343 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:16,346 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 99 +galaxy.jobs DEBUG 2024-09-03 06:51:16,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [99] prepared (73.327 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:51:16,448 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/99/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/99/registry.xml' '/galaxy/server/database/jobs_directory/000/99/upload_params.json' '116:/galaxy/server/database/objects/4/e/c/dataset_4ecc3370-657d-4bce-9ffc-e782456005e0_files:/galaxy/server/database/objects/4/e/c/dataset_4ecc3370-657d-4bce-9ffc-e782456005e0.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:51:16,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (99) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/99/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/99/galaxy_99.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:16,470 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 99 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:16,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 99 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:17,171 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-09-03 06:51:17,347 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 101, 100 +tpv.core.entities DEBUG 2024-09-03 06:51:17,371 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:51:17,372 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:51:17,375 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:51:17,386 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:51:17,401 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Working directory for job is: /galaxy/server/database/jobs_directory/000/100 +galaxy.jobs.runners DEBUG 2024-09-03 06:51:17,408 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [100] queued (33.013 ms) +galaxy.jobs.handler INFO 2024-09-03 06:51:17,411 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:17,414 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 100 +tpv.core.entities DEBUG 2024-09-03 06:51:17,419 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:51:17,420 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:51:17,424 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:51:17,433 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:51:17,458 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Working directory for job is: /galaxy/server/database/jobs_directory/000/101 +galaxy.jobs.runners DEBUG 2024-09-03 06:51:17,466 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [101] queued (42.321 ms) +galaxy.jobs.handler INFO 2024-09-03 06:51:17,468 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:17,472 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 101 +galaxy.jobs DEBUG 2024-09-03 06:51:17,519 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [100] prepared (96.214 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:51:17,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '117:/galaxy/server/database/objects/a/f/0/dataset_af02b0d6-f8d9-4fe6-8dca-f1ec2f021123_files:/galaxy/server/database/objects/a/f/0/dataset_af02b0d6-f8d9-4fe6-8dca-f1ec2f021123.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:51:17,553 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs DEBUG 2024-09-03 06:51:17,563 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [101] prepared (79.620 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:17,572 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 100 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-09-03 06:51:17,586 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/101/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/101/registry.xml' '/galaxy/server/database/jobs_directory/000/101/upload_params.json' '118:/galaxy/server/database/objects/a/4/9/dataset_a49ab179-6cd5-49cf-ad79-3281eb33819e_files:/galaxy/server/database/objects/a/4/9/dataset_a49ab179-6cd5-49cf-ad79-3281eb33819e.dat'] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:17,588 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 100 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-09-03 06:51:17,603 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (101) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/101/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/101/galaxy_101.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:17,624 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 101 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:17,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 101 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:18,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:18,261 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:26,601 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-cnrb8 with k8s id: gxy-cnrb8 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:51:26,737 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 99: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:27,643 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-rd8jx with k8s id: gxy-rd8jx succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:27,656 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-wl56z with k8s id: gxy-wl56z succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:51:27,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 100: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:51:27,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 101: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.runners DEBUG 2024-09-03 06:51:37,267 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 99 finished +galaxy.model.metadata DEBUG 2024-09-03 06:51:37,311 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 116 +galaxy.jobs INFO 2024-09-03 06:51:37,369 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 99 in /galaxy/server/database/jobs_directory/000/99 +galaxy.jobs DEBUG 2024-09-03 06:51:37,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 99 executed (129.942 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:37,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 99 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-09-03 06:51:38,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 100 finished +galaxy.model.metadata DEBUG 2024-09-03 06:51:38,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 117 +galaxy.jobs INFO 2024-09-03 06:51:38,452 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 100 in /galaxy/server/database/jobs_directory/000/100 +galaxy.jobs.runners DEBUG 2024-09-03 06:51:38,459 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 101 finished +galaxy.model.metadata DEBUG 2024-09-03 06:51:38,498 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 118 +galaxy.jobs DEBUG 2024-09-03 06:51:38,523 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 100 executed (115.790 ms) +galaxy.jobs INFO 2024-09-03 06:51:38,527 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 101 in /galaxy/server/database/jobs_directory/000/101 +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:38,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 100 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-09-03 06:51:38,581 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 101 executed (103.406 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:38,595 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 101 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:51:39,004 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 102 +tpv.core.entities DEBUG 2024-09-03 06:51:39,031 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:51:39,031 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:51:39,034 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:51:39,045 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:51:39,059 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Working directory for job is: /galaxy/server/database/jobs_directory/000/102 +galaxy.jobs.runners DEBUG 2024-09-03 06:51:39,069 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [102] queued (34.559 ms) +galaxy.jobs.handler INFO 2024-09-03 06:51:39,071 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:39,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 102 +galaxy.jobs DEBUG 2024-09-03 06:51:39,136 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [102] prepared (54.309 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:51:39,136 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:51:39,136 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:51:39,159 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:51:39,178 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/102/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/4/e/c/dataset_4ecc3370-657d-4bce-9ffc-e782456005e0.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . '/galaxy/server/database/objects/a/f/0/dataset_af02b0d6-f8d9-4fe6-8dca-f1ec2f021123.dat' '/galaxy/server/database/objects/a/4/9/dataset_a49ab179-6cd5-49cf-ad79-3281eb33819e.dat' && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi] +galaxy.jobs.runners DEBUG 2024-09-03 06:51:39,188 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (102) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/102/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/102/galaxy_102.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:39,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 102 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:51:39,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:51:39,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1: mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:51:39,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-143e618e2d6eef454186ce14739a2cabc5ecf645:98aaf7a4902bd7819cc39c943cb2ccd018ec6f95-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:39,241 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 102 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:39,699 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:43,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-fkxpc with k8s id: gxy-fkxpc succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:51:43,911 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 102: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:51:51,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 102 finished +galaxy.model.metadata DEBUG 2024-09-03 06:51:51,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 119 +galaxy.jobs INFO 2024-09-03 06:51:51,373 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 102 in /galaxy/server/database/jobs_directory/000/102 +galaxy.jobs DEBUG 2024-09-03 06:51:51,398 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 102 executed (331.010 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:51,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 102 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:51:53,306 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 103, 104 +tpv.core.entities DEBUG 2024-09-03 06:51:53,333 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:51:53,334 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:51:53,337 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:51:53,349 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:51:53,364 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Working directory for job is: /galaxy/server/database/jobs_directory/000/103 +galaxy.jobs.runners DEBUG 2024-09-03 06:51:53,372 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [103] queued (34.131 ms) +galaxy.jobs.handler INFO 2024-09-03 06:51:53,374 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:53,378 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 103 +tpv.core.entities DEBUG 2024-09-03 06:51:53,388 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:51:53,389 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:51:53,392 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:51:53,404 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:51:53,429 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Working directory for job is: /galaxy/server/database/jobs_directory/000/104 +galaxy.jobs.runners DEBUG 2024-09-03 06:51:53,437 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [104] queued (44.389 ms) +galaxy.jobs.handler INFO 2024-09-03 06:51:53,439 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:53,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 104 +galaxy.jobs DEBUG 2024-09-03 06:51:53,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [103] prepared (94.111 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:51:53,508 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/103/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/103/registry.xml' '/galaxy/server/database/jobs_directory/000/103/upload_params.json' '125:/galaxy/server/database/objects/a/1/0/dataset_a1059f17-9a4c-401a-9d48-bc62fa4aab6e_files:/galaxy/server/database/objects/a/1/0/dataset_a1059f17-9a4c-401a-9d48-bc62fa4aab6e.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:51:53,519 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (103) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/103/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/103/galaxy_103.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-09-03 06:51:53,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [104] prepared (79.129 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:53,534 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 103 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:53,548 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 103 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-09-03 06:51:53,553 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/104/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/104/registry.xml' '/galaxy/server/database/jobs_directory/000/104/upload_params.json' '126:/galaxy/server/database/objects/3/8/3/dataset_3831c82d-3966-4acf-897b-5a187314bc47_files:/galaxy/server/database/objects/3/8/3/dataset_3831c82d-3966-4acf-897b-5a187314bc47.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:51:53,562 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (104) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/104/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/104/galaxy_104.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:53,578 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 104 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:53,590 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 104 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:53,803 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:51:53,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:03,057 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-pkbst with k8s id: gxy-pkbst succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:03,069 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-r58tn with k8s id: gxy-r58tn succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:52:03,208 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 104: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:52:03,220 [pN:job_handler_0,p:8,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 2024-09-03 06:52:10,671 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 103 finished +galaxy.jobs.runners DEBUG 2024-09-03 06:52:10,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 104 finished +galaxy.model.metadata DEBUG 2024-09-03 06:52:10,716 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 125 +galaxy.model.metadata DEBUG 2024-09-03 06:52:10,730 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 126 +galaxy.jobs INFO 2024-09-03 06:52:10,751 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 103 in /galaxy/server/database/jobs_directory/000/103 +galaxy.jobs INFO 2024-09-03 06:52:10,771 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 104 in /galaxy/server/database/jobs_directory/000/104 +galaxy.jobs DEBUG 2024-09-03 06:52:10,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 103 executed (118.596 ms) +galaxy.jobs DEBUG 2024-09-03 06:52:10,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 104 executed (112.377 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:10,825 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 103 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:10,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 104 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:52:12,798 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 106, 105 +tpv.core.entities DEBUG 2024-09-03 06:52:12,827 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:52:12,828 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:52:12,832 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:52:12,843 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:52:12,857 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Working directory for job is: /galaxy/server/database/jobs_directory/000/105 +galaxy.jobs.runners DEBUG 2024-09-03 06:52:12,866 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [105] queued (34.071 ms) +galaxy.jobs.handler INFO 2024-09-03 06:52:12,868 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:12,872 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 105 +tpv.core.entities DEBUG 2024-09-03 06:52:12,881 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:52:12,882 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:52:12,887 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:52:12,902 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:52:12,926 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Working directory for job is: /galaxy/server/database/jobs_directory/000/106 +galaxy.jobs.runners DEBUG 2024-09-03 06:52:12,933 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [106] queued (46.158 ms) +galaxy.jobs.handler INFO 2024-09-03 06:52:12,936 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:12,939 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 106 +galaxy.jobs DEBUG 2024-09-03 06:52:12,985 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [105] prepared (99.669 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:52:13,007 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/105/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/105/registry.xml' '/galaxy/server/database/jobs_directory/000/105/upload_params.json' '127:/galaxy/server/database/objects/0/6/5/dataset_06523432-b9d1-4891-b7d3-e4f400182d1f_files:/galaxy/server/database/objects/0/6/5/dataset_06523432-b9d1-4891-b7d3-e4f400182d1f.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:52:13,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (105) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/105/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/105/galaxy_105.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-09-03 06:52:13,030 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [106] prepared (81.282 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:13,034 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 105 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:13,047 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 105 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-09-03 06:52:13,053 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/106/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/106/registry.xml' '/galaxy/server/database/jobs_directory/000/106/upload_params.json' '128:/galaxy/server/database/objects/3/b/b/dataset_3bb2da50-e1ca-44ce-a322-d63f5df29347_files:/galaxy/server/database/objects/3/b/b/dataset_3bb2da50-e1ca-44ce-a322-d63f5df29347.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:52:13,063 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (106) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/106/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/106/galaxy_106.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:13,081 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 106 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:13,096 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 106 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:14,114 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:14,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:22,378 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-gf269 with k8s id: gxy-gf269 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:52:22,494 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 106: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:23,395 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-2v4x5 with k8s id: gxy-2v4x5 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:52:23,521 [pN:job_handler_0,p:8,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 2024-09-03 06:52:29,941 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 106 finished +galaxy.model.metadata DEBUG 2024-09-03 06:52:29,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 128 +galaxy.jobs INFO 2024-09-03 06:52:30,021 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 106 in /galaxy/server/database/jobs_directory/000/106 +galaxy.jobs DEBUG 2024-09-03 06:52:30,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 106 executed (117.944 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:30,092 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 106 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-09-03 06:52:31,020 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 105 finished +galaxy.model.metadata DEBUG 2024-09-03 06:52:31,065 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 127 +galaxy.jobs INFO 2024-09-03 06:52:31,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 105 in /galaxy/server/database/jobs_directory/000/105 +galaxy.jobs DEBUG 2024-09-03 06:52:31,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 105 executed (120.353 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:31,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 105 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:52:32,308 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 107 +tpv.core.entities DEBUG 2024-09-03 06:52:32,333 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:52:32,333 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:52:32,338 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:52:32,349 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:52:32,362 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Working directory for job is: /galaxy/server/database/jobs_directory/000/107 +galaxy.jobs.runners DEBUG 2024-09-03 06:52:32,369 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [107] queued (31.528 ms) +galaxy.jobs.handler INFO 2024-09-03 06:52:32,371 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:32,374 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 107 +galaxy.jobs DEBUG 2024-09-03 06:52:32,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [107] prepared (63.808 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:52:32,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:52:32,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3: samtools:0.1.16 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:52:32,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:0.1.16,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:52:32,708 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/107/tool_script.sh] for tool command [ln -s '/galaxy/server/database/objects/0/6/5/dataset_06523432-b9d1-4891-b7d3-e4f400182d1f.dat' input1.bam && ln -s '/galaxy/server/database/objects/_metadata_files/8/5/3/metadata_853b3ca5-b2b1-4b83-8363-91890d787490.dat' 'input1.bam.bai' && ln -s '/galaxy/server/database/objects/3/b/b/dataset_3bb2da50-e1ca-44ce-a322-d63f5df29347.dat' reference.fasta && samtools faidx reference.fasta && samtools pileup -M 60 -f reference.fasta input1.bam > '/galaxy/server/database/objects/6/e/a/dataset_6eae9bca-de3a-49f3-a1fe-3848034e3fd9.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:52:32,717 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (107) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/107/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/107/galaxy_107.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:32,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 107 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:52:32,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:52:32,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3: samtools:0.1.16 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:52:32,757 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:0.1.16,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:32,781 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 107 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:33,429 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:38,514 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-kc4wx failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:38,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:38,534 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job: gxy-kc4wx failed due to an unknown exit code from the tool. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:38,539 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 107 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-09-03 06:52:38,739 [pN:job_handler_0,p:8,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 2024-09-03 06:52:46,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 107 finished +galaxy.tool_util.output_checker INFO 2024-09-03 06:52:46,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job error detected, failing job. Reasons are [{'type': 'exit_code', 'desc': 'Fatal error: Exit code 127 ()', 'exit_code': 127, 'code_desc': '', 'error_level': 3}] +galaxy.jobs DEBUG 2024-09-03 06:52:46,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (107) setting dataset 129 state to ERROR +galaxy.jobs INFO 2024-09-03 06:52:46,148 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 107 in /galaxy/server/database/jobs_directory/000/107 +galaxy.jobs DEBUG 2024-09-03 06:52:46,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 107 executed (121.217 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:46,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 107 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:52:48,635 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 109, 108 +tpv.core.entities DEBUG 2024-09-03 06:52:48,659 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:52:48,660 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:52:48,663 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:52:48,672 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:52:48,688 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Working directory for job is: /galaxy/server/database/jobs_directory/000/108 +galaxy.jobs.runners DEBUG 2024-09-03 06:52:48,696 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [108] queued (32.625 ms) +galaxy.jobs.handler INFO 2024-09-03 06:52:48,699 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:48,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 108 +tpv.core.entities DEBUG 2024-09-03 06:52:48,711 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:52:48,712 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:52:48,717 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:52:48,728 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:52:48,762 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Working directory for job is: /galaxy/server/database/jobs_directory/000/109 +galaxy.jobs.runners DEBUG 2024-09-03 06:52:48,772 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [109] queued (54.893 ms) +galaxy.jobs.handler INFO 2024-09-03 06:52:48,774 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:48,778 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 109 +galaxy.jobs DEBUG 2024-09-03 06:52:48,816 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [108] prepared (101.084 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:52:48,850 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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' '130:/galaxy/server/database/objects/1/5/2/dataset_1526ed88-17bf-470b-8044-87a12f5dc1f4_files:/galaxy/server/database/objects/1/5/2/dataset_1526ed88-17bf-470b-8044-87a12f5dc1f4.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:52:48,861 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs DEBUG 2024-09-03 06:52:48,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [109] prepared (88.052 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:48,879 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 108 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:48,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 108 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-09-03 06:52:48,900 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/109/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/109/registry.xml' '/galaxy/server/database/jobs_directory/000/109/upload_params.json' '131:/galaxy/server/database/objects/5/c/5/dataset_5c5c06e5-29d0-49a7-b55c-fdfb5baadff9_files:/galaxy/server/database/objects/5/c/5/dataset_5c5c06e5-29d0-49a7-b55c-fdfb5baadff9.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:52:48,910 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (109) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/109/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/109/galaxy_109.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:48,925 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 109 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:48,938 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 109 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:49,643 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:49,677 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:52:59,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-wqwhf with k8s id: gxy-wqwhf succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:52:59,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 109: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:00,086 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-n6q4b with k8s id: gxy-n6q4b succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:53:00,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 108: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:53:06,722 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 109 finished +galaxy.model.metadata DEBUG 2024-09-03 06:53:06,761 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 131 +galaxy.jobs INFO 2024-09-03 06:53:06,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 109 in /galaxy/server/database/jobs_directory/000/109 +galaxy.jobs DEBUG 2024-09-03 06:53:06,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 109 executed (100.165 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:06,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 109 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-09-03 06:53:07,746 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 108 finished +galaxy.model.metadata DEBUG 2024-09-03 06:53:07,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 130 +galaxy.jobs INFO 2024-09-03 06:53:07,827 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 108 in /galaxy/server/database/jobs_directory/000/108 +galaxy.jobs DEBUG 2024-09-03 06:53:07,867 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 108 executed (100.926 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:07,911 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 108 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:53:09,212 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 110 +tpv.core.entities DEBUG 2024-09-03 06:53:09,241 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:53:09,241 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:53:09,245 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:53:09,253 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:53:09,280 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Working directory for job is: /galaxy/server/database/jobs_directory/000/110 +galaxy.jobs.runners DEBUG 2024-09-03 06:53:09,289 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [110] queued (44.124 ms) +galaxy.jobs.handler INFO 2024-09-03 06:53:09,291 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:09,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 110 +galaxy.jobs DEBUG 2024-09-03 06:53:09,351 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [110] prepared (48.177 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:53:09,351 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:53:09,351 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:53:09,378 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:53:09,398 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/110/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/110/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/5/c/5/dataset_5c5c06e5-29d0-49a7-b55c-fdfb5baadff9.dat' ref.fa && samtools faidx ref.fa && samtools calmd -b -@ $addthreads '/galaxy/server/database/objects/1/5/2/dataset_1526ed88-17bf-470b-8044-87a12f5dc1f4.dat' 'ref.fa' > '/galaxy/server/database/objects/a/1/f/dataset_a1fac533-fc32-4d7b-9232-92e21a19d0cc.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:53:09,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (110) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:09,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 110 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:53:09,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:53:09,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:53:09,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:09,458 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 110 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:10,112 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:17,221 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-xnc4c with k8s id: gxy-xnc4c succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:53:17,350 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 110: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:53:24,357 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 110 finished +galaxy.model.metadata DEBUG 2024-09-03 06:53:24,400 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 132 +galaxy.jobs INFO 2024-09-03 06:53:24,436 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 110 in /galaxy/server/database/jobs_directory/000/110 +galaxy.jobs DEBUG 2024-09-03 06:53:24,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 110 executed (98.434 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:24,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 110 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:53:26,564 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 112, 111 +tpv.core.entities DEBUG 2024-09-03 06:53:26,590 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:53:26,590 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:53:26,594 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:53:26,609 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:53:26,624 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Working directory for job is: /galaxy/server/database/jobs_directory/000/111 +galaxy.jobs.runners DEBUG 2024-09-03 06:53:26,630 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [111] queued (35.651 ms) +galaxy.jobs.handler INFO 2024-09-03 06:53:26,632 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:26,635 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 111 +tpv.core.entities DEBUG 2024-09-03 06:53:26,644 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:53:26,644 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:53:26,648 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:53:26,659 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:53:26,684 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Working directory for job is: /galaxy/server/database/jobs_directory/000/112 +galaxy.jobs.runners DEBUG 2024-09-03 06:53:26,694 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [112] queued (46.052 ms) +galaxy.jobs.handler INFO 2024-09-03 06:53:26,697 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:26,701 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 112 +galaxy.jobs DEBUG 2024-09-03 06:53:26,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [111] prepared (90.386 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:53:26,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/111/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/111/registry.xml' '/galaxy/server/database/jobs_directory/000/111/upload_params.json' '133:/galaxy/server/database/objects/5/b/d/dataset_5bd7e051-2ba9-48e1-9fd0-7542ac9bf44d_files:/galaxy/server/database/objects/5/b/d/dataset_5bd7e051-2ba9-48e1-9fd0-7542ac9bf44d.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:53:26,783 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (111) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/111/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/111/galaxy_111.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-09-03 06:53:26,790 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [112] prepared (80.687 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:26,804 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 111 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-09-03 06:53:26,815 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/112/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/112/registry.xml' '/galaxy/server/database/jobs_directory/000/112/upload_params.json' '134:/galaxy/server/database/objects/b/a/0/dataset_ba0e9406-5672-47d8-9e02-7fb57f928309_files:/galaxy/server/database/objects/b/a/0/dataset_ba0e9406-5672-47d8-9e02-7fb57f928309.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:53:26,826 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (112) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/112/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/112/galaxy_112.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:26,833 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 111 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:26,844 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 112 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:26,859 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 112 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:27,259 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:27,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:36,493 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-2kdsx with k8s id: gxy-2kdsx succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:36,512 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-wgj2t with k8s id: gxy-wgj2t succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:53:36,634 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 111: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:53:36,657 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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 2024-09-03 06:53:43,923 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 111 finished +galaxy.model.metadata DEBUG 2024-09-03 06:53:43,960 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 133 +galaxy.jobs.runners DEBUG 2024-09-03 06:53:43,968 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 112 finished +galaxy.jobs INFO 2024-09-03 06:53:44,013 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 111 in /galaxy/server/database/jobs_directory/000/111 +galaxy.model.metadata DEBUG 2024-09-03 06:53:44,030 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 134 +galaxy.jobs INFO 2024-09-03 06:53:44,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 112 in /galaxy/server/database/jobs_directory/000/112 +galaxy.jobs DEBUG 2024-09-03 06:53:44,075 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 111 executed (133.900 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:44,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 111 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-09-03 06:53:44,110 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 112 executed (104.139 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:44,130 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 112 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:53:45,004 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 113 +tpv.core.entities DEBUG 2024-09-03 06:53:45,033 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:53:45,033 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:53:45,037 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:53:45,048 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:53:45,060 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Working directory for job is: /galaxy/server/database/jobs_directory/000/113 +galaxy.jobs.runners DEBUG 2024-09-03 06:53:45,067 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [113] queued (30.357 ms) +galaxy.jobs.handler INFO 2024-09-03 06:53:45,069 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:45,072 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 113 +galaxy.jobs DEBUG 2024-09-03 06:53:45,113 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [113] prepared (34.287 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:53:45,113 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:53:45,113 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:53:45,372 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:53:45,396 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/113/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/113/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/b/a/0/dataset_ba0e9406-5672-47d8-9e02-7fb57f928309.dat' ref.fa && samtools faidx ref.fa && samtools calmd -r -E -e -C 50 -b -@ $addthreads '/galaxy/server/database/objects/5/b/d/dataset_5bd7e051-2ba9-48e1-9fd0-7542ac9bf44d.dat' 'ref.fa' > '/galaxy/server/database/objects/1/d/f/dataset_1dffe831-e25d-485a-8753-29acc8f63ce0.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:53:45,413 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (113) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/113/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/113/galaxy_113.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:45,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 113 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:53:45,438 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:53:45,438 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:53:45,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:45,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 113 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:45,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:49,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-76826 with k8s id: gxy-76826 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:53:49,797 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 113: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:53:56,944 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 113 finished +galaxy.model.metadata DEBUG 2024-09-03 06:53:56,988 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 135 +galaxy.jobs INFO 2024-09-03 06:53:57,028 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 113 in /galaxy/server/database/jobs_directory/000/113 +galaxy.jobs DEBUG 2024-09-03 06:53:57,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 113 executed (106.816 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:53:57,086 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 113 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:54:01,344 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 114 +tpv.core.entities DEBUG 2024-09-03 06:54:01,371 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:54:01,371 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:54:01,375 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:54:01,386 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:54:01,402 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Working directory for job is: /galaxy/server/database/jobs_directory/000/114 +galaxy.jobs.runners DEBUG 2024-09-03 06:54:01,409 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [114] queued (34.081 ms) +galaxy.jobs.handler INFO 2024-09-03 06:54:01,412 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:54:01,414 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 114 +galaxy.jobs DEBUG 2024-09-03 06:54:01,502 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [114] prepared (79.377 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:54:01,524 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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' '136:/galaxy/server/database/objects/6/1/7/dataset_617c26fe-6b3d-4954-89e5-15a4a4f15548_files:/galaxy/server/database/objects/6/1/7/dataset_617c26fe-6b3d-4954-89e5-15a4a4f15548.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:54:01,532 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (114) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/114/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/114/galaxy_114.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:54:01,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 114 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:54:01,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 114 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:54:01,692 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:54:10,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-q526g with k8s id: gxy-q526g succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:54:10,997 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 114: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:54:18,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 114 finished +galaxy.model.metadata DEBUG 2024-09-03 06:54:18,081 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 136 +galaxy.jobs INFO 2024-09-03 06:54:18,110 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 114 in /galaxy/server/database/jobs_directory/000/114 +galaxy.jobs DEBUG 2024-09-03 06:54:18,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 114 executed (104.659 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:54:18,173 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 114 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:54:18,809 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 115 +tpv.core.entities DEBUG 2024-09-03 06:54:18,835 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:54:18,836 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:54:18,839 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:54:18,847 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:54:18,859 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Working directory for job is: /galaxy/server/database/jobs_directory/000/115 +galaxy.jobs.runners DEBUG 2024-09-03 06:54:18,865 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [115] queued (26.378 ms) +galaxy.jobs.handler INFO 2024-09-03 06:54:18,869 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:54:18,870 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 115 +galaxy.jobs DEBUG 2024-09-03 06:54:18,921 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [115] prepared (42.061 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:54:18,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:54:18,922 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2: mulled-v2-73a2658554da0b18a11a585a481ae725b820e94a:bc2e569e2a76e9ab09523a345979924ab514ebe9 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:54:19,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-73a2658554da0b18a11a585a481ae725b820e94a:bc2e569e2a76e9ab09523a345979924ab514ebe9-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:54:19,133 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/115/tool_script.sh] for tool command [Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/058b40656107/scater_plot_exprs_freq/scater-plot-exprs-freq.R' -i '/galaxy/server/database/objects/6/1/7/dataset_617c26fe-6b3d-4954-89e5-15a4a4f15548.dat' -o '/galaxy/server/database/objects/6/5/d/dataset_65dc56e6-ff07-411e-a868-68a8e43e3adf.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:54:19,142 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (115) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/115/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/115/galaxy_115.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:54:19,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 115 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:54:19,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:54:19,157 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2: mulled-v2-73a2658554da0b18a11a585a481ae725b820e94a:bc2e569e2a76e9ab09523a345979924ab514ebe9 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:54:19,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-73a2658554da0b18a11a585a481ae725b820e94a:bc2e569e2a76e9ab09523a345979924ab514ebe9-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:54:19,193 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 115 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:54:19,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:54:54,464 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-zltsp with k8s id: gxy-zltsp succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:54:54,597 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 115: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:55:01,536 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 115 finished +galaxy.model.metadata DEBUG 2024-09-03 06:55:01,588 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 137 +galaxy.jobs INFO 2024-09-03 06:55:01,622 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 115 in /galaxy/server/database/jobs_directory/000/115 +galaxy.jobs DEBUG 2024-09-03 06:55:01,671 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 115 executed (107.612 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:01,683 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 115 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:55:03,592 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 116 +tpv.core.entities DEBUG 2024-09-03 06:55:03,623 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:55:03,623 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:55:03,627 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:55:03,637 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:55:03,647 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Working directory for job is: /galaxy/server/database/jobs_directory/000/116 +galaxy.jobs.runners DEBUG 2024-09-03 06:55:03,652 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [116] queued (25.137 ms) +galaxy.jobs.handler INFO 2024-09-03 06:55:03,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:03,657 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 116 +galaxy.jobs DEBUG 2024-09-03 06:55:03,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [116] prepared (35.651 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:55:03,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:55:03,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0: bioconductor-rtracklayer:1.42.1 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:55:03,909 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/bioconductor-rtracklayer:1.42.1--r351h9d9f1b6_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:55:03,931 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/116/tool_script.sh] for tool command [mkdir outputs; for param in $(echo '1, 5, 10' | sed 's/,/ /g'); do echo $param > outputs/'perplexity'_$param\.txt; done] +galaxy.jobs.runners DEBUG 2024-09-03 06:55:03,946 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (116) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/116/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/116/galaxy_116.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:03,963 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 116 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:55:03,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:55:03,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0: bioconductor-rtracklayer:1.42.1 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:55:03,992 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/bioconductor-rtracklayer:1.42.1--r351h9d9f1b6_1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:04,011 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 116 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:04,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:29,951 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-n4cn7 with k8s id: gxy-n4cn7 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:55:30,058 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 116: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:55:37,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 116 finished +galaxy.model.store.discover DEBUG 2024-09-03 06:55:37,079 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (116) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/116/working/outputs/perplexity_1.txt] with element identifier [perplexity_1] for output [parameter_iteration] (8.433 ms) +galaxy.model.store.discover DEBUG 2024-09-03 06:55:37,079 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (116) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/116/working/outputs/perplexity_10.txt] with element identifier [perplexity_10] for output [parameter_iteration] (0.631 ms) +galaxy.model.store.discover DEBUG 2024-09-03 06:55:37,080 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (116) Created dynamic collection dataset for path [/galaxy/server/database/jobs_directory/000/116/working/outputs/perplexity_5.txt] with element identifier [perplexity_5] for output [parameter_iteration] (0.587 ms) +galaxy.model.store.discover DEBUG 2024-09-03 06:55:37,115 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (116) Add dynamic collection datasets to history for output [parameter_iteration] (34.963 ms) +galaxy.jobs INFO 2024-09-03 06:55:37,179 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 116 in /galaxy/server/database/jobs_directory/000/116 +galaxy.jobs DEBUG 2024-09-03 06:55:37,209 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 116 executed (155.883 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:37,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 116 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:55:39,233 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 117 +tpv.core.entities DEBUG 2024-09-03 06:55:39,254 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:55:39,254 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:55:39,257 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:55:39,266 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:55:39,277 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Working directory for job is: /galaxy/server/database/jobs_directory/000/117 +galaxy.jobs.runners DEBUG 2024-09-03 06:55:39,284 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [117] queued (26.381 ms) +galaxy.jobs.handler INFO 2024-09-03 06:55:39,286 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:39,289 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 117 +galaxy.jobs DEBUG 2024-09-03 06:55:39,372 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [117] prepared (73.505 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:55:39,393 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/117/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/117/registry.xml' '/galaxy/server/database/jobs_directory/000/117/upload_params.json' '141:/galaxy/server/database/objects/d/c/0/dataset_dc00c48c-ea9f-48d2-b764-04f2c1d17455_files:/galaxy/server/database/objects/d/c/0/dataset_dc00c48c-ea9f-48d2-b764-04f2c1d17455.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:55:39,401 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (117) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/117/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/117/galaxy_117.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:39,413 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 117 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:39,425 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 117 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:39,974 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-09-03 06:55:40,290 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 118 +tpv.core.entities DEBUG 2024-09-03 06:55:40,312 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:55:40,312 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:55:40,316 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:55:40,325 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:55:40,336 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Working directory for job is: /galaxy/server/database/jobs_directory/000/118 +galaxy.jobs.runners DEBUG 2024-09-03 06:55:40,342 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [118] queued (26.184 ms) +galaxy.jobs.handler INFO 2024-09-03 06:55:40,344 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:40,346 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 118 +galaxy.jobs DEBUG 2024-09-03 06:55:40,414 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [118] prepared (60.950 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:55:40,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/118/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/118/registry.xml' '/galaxy/server/database/jobs_directory/000/118/upload_params.json' '142:/galaxy/server/database/objects/1/8/b/dataset_18b8f8af-00c8-4e1c-82a9-8d3698ebc4e8_files:/galaxy/server/database/objects/1/8/b/dataset_18b8f8af-00c8-4e1c-82a9-8d3698ebc4e8.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:55:40,437 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (118) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/118/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/118/galaxy_118.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:40,449 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 118 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:40,460 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 118 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:41,016 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:49,199 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-7pvwz with k8s id: gxy-7pvwz succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:55:49,337 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 117: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.kubernetes DEBUG 2024-09-03 06:55:50,226 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-mvrct with k8s id: gxy-mvrct succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:55:50,353 [pN:job_handler_0,p:8,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 2024-09-03 06:55:56,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 117 finished +galaxy.model.metadata DEBUG 2024-09-03 06:55:57,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 141 +galaxy.jobs INFO 2024-09-03 06:55:57,054 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 117 in /galaxy/server/database/jobs_directory/000/117 +galaxy.jobs DEBUG 2024-09-03 06:55:57,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 117 executed (106.707 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:57,117 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 117 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-09-03 06:55:57,774 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 118 finished +galaxy.model.metadata DEBUG 2024-09-03 06:55:57,815 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 142 +galaxy.jobs INFO 2024-09-03 06:55:57,846 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 118 in /galaxy/server/database/jobs_directory/000/118 +galaxy.jobs DEBUG 2024-09-03 06:55:57,897 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 118 executed (104.269 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:57,910 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 118 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:55:58,701 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 119 +tpv.core.entities DEBUG 2024-09-03 06:55:58,726 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:55:58,726 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:55:58,730 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:55:58,739 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:55:58,753 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Working directory for job is: /galaxy/server/database/jobs_directory/000/119 +galaxy.jobs.runners DEBUG 2024-09-03 06:55:58,762 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [119] queued (32.206 ms) +galaxy.jobs.handler INFO 2024-09-03 06:55:58,765 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:58,767 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 119 +galaxy.security.object_wrapper WARNING 2024-09-03 06:55:58,808 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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.jobs DEBUG 2024-09-03 06:55:58,879 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [119] prepared (103.380 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:55:58,880 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:55:58,880 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:55:59,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:55:59,099 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/119/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/119/configs/tmp28verjg1' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/119/configs/tmpgu1n986b' -Q '/galaxy/server/database/jobs_directory/000/119/configs/tmp28verjg1' --comment_char='#' -o '/galaxy/server/database/objects/5/2/0/dataset_52030cdc-5db4-40ef-a23c-b54abb545198.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:55:59,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (119) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/119/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/119/galaxy_119.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:59,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 119 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:55:59,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:55:59,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:55:59,145 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:55:59,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 119 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:00,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:08,586 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-6l6bt with k8s id: gxy-6l6bt succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:56:08,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 119: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:56:15,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 119 finished +galaxy.model.metadata DEBUG 2024-09-03 06:56:15,815 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 143 +galaxy.jobs INFO 2024-09-03 06:56:15,874 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 119 in /galaxy/server/database/jobs_directory/000/119 +galaxy.jobs DEBUG 2024-09-03 06:56:15,920 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 119 executed (125.883 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:15,937 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 119 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:56:17,049 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 121, 120 +tpv.core.entities DEBUG 2024-09-03 06:56:17,074 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:56:17,074 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:56:17,077 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:56:17,087 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:56:17,100 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Working directory for job is: /galaxy/server/database/jobs_directory/000/120 +galaxy.jobs.runners DEBUG 2024-09-03 06:56:17,106 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [120] queued (29.137 ms) +galaxy.jobs.handler INFO 2024-09-03 06:56:17,108 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:17,111 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 120 +tpv.core.entities DEBUG 2024-09-03 06:56:17,119 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:56:17,119 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:56:17,124 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:56:17,137 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:56:17,164 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Working directory for job is: /galaxy/server/database/jobs_directory/000/121 +galaxy.jobs.runners DEBUG 2024-09-03 06:56:17,173 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [121] queued (48.704 ms) +galaxy.jobs.handler INFO 2024-09-03 06:56:17,175 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:17,178 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 121 +galaxy.jobs DEBUG 2024-09-03 06:56:17,233 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [120] prepared (107.578 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:56:17,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/120/tool_script.sh] for tool command [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' '144:/galaxy/server/database/objects/d/b/9/dataset_db9be421-2bb2-4119-8158-f2d61f86df8b_files:/galaxy/server/database/objects/d/b/9/dataset_db9be421-2bb2-4119-8158-f2d61f86df8b.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:56:17,265 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (120) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/120/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/120/galaxy_120.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-09-03 06:56:17,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [121] prepared (84.607 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:17,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 120 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:17,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 120 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-09-03 06:56:17,303 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/121/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/121/registry.xml' '/galaxy/server/database/jobs_directory/000/121/upload_params.json' '145:/galaxy/server/database/objects/5/3/7/dataset_537ac4c1-04d8-4baf-8989-6e0ff7a1ffad_files:/galaxy/server/database/objects/5/3/7/dataset_537ac4c1-04d8-4baf-8989-6e0ff7a1ffad.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:56:17,316 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (121) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/121/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/121/galaxy_121.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:17,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 121 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:17,342 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 121 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:17,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:17,648 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:27,050 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-f6r2r with k8s id: gxy-f6r2r succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:27,061 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-kjnhx with k8s id: gxy-kjnhx succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:56:27,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 120: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:56:27,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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 2024-09-03 06:56:34,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 121 finished +galaxy.model.metadata DEBUG 2024-09-03 06:56:34,400 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 145 +galaxy.jobs.runners DEBUG 2024-09-03 06:56:34,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 120 finished +galaxy.jobs INFO 2024-09-03 06:56:34,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 121 in /galaxy/server/database/jobs_directory/000/121 +galaxy.model.metadata DEBUG 2024-09-03 06:56:34,470 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 144 +galaxy.jobs INFO 2024-09-03 06:56:34,502 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 120 in /galaxy/server/database/jobs_directory/000/120 +galaxy.jobs DEBUG 2024-09-03 06:56:34,504 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 121 executed (126.401 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:34,519 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 121 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-09-03 06:56:34,557 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 120 executed (117.902 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:34,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 120 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:56:35,470 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 122 +tpv.core.entities DEBUG 2024-09-03 06:56:35,499 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:56:35,499 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:56:35,503 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:56:35,514 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:56:35,527 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Working directory for job is: /galaxy/server/database/jobs_directory/000/122 +galaxy.jobs.runners DEBUG 2024-09-03 06:56:35,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [122] queued (34.239 ms) +galaxy.jobs.handler INFO 2024-09-03 06:56:35,539 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:35,541 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 122 +galaxy.jobs DEBUG 2024-09-03 06:56:35,618 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [122] prepared (67.209 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:56:35,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:56:35,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:56:35,641 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:56:35,665 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/122/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/122/configs/tmpm9lf6m4t' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/122/configs/tmp6ur0tthu' -Q '/galaxy/server/database/jobs_directory/000/122/configs/tmpm9lf6m4t' --comment_char='#' -o '/galaxy/server/database/objects/0/c/7/dataset_0c77895f-3af5-4f9f-bec2-42f2fb536d37.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:56:35,674 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (122) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/122/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/122/galaxy_122.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:35,687 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 122 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:56:35,687 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:56:35,687 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:56:35,706 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:35,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 122 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:36,181 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:40,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ggtwn with k8s id: gxy-ggtwn succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:56:40,378 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 122: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:56:47,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 122 finished +galaxy.model.metadata DEBUG 2024-09-03 06:56:47,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 146 +galaxy.jobs INFO 2024-09-03 06:56:47,493 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 122 in /galaxy/server/database/jobs_directory/000/122 +galaxy.jobs DEBUG 2024-09-03 06:56:47,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 122 executed (89.842 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:47,541 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 122 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:56:48,744 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 123 +tpv.core.entities DEBUG 2024-09-03 06:56:48,770 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:56:48,771 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:56:48,775 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:56:48,787 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:56:48,802 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Working directory for job is: /galaxy/server/database/jobs_directory/000/123 +galaxy.jobs.runners DEBUG 2024-09-03 06:56:48,809 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [123] queued (34.137 ms) +galaxy.jobs.handler INFO 2024-09-03 06:56:48,811 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:48,813 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 123 +galaxy.jobs DEBUG 2024-09-03 06:56:48,893 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [123] prepared (70.418 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:56:48,912 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '147:/galaxy/server/database/objects/d/1/8/dataset_d18ac2ec-a43f-4d3f-b1ae-f4e57da5f55f_files:/galaxy/server/database/objects/d/1/8/dataset_d18ac2ec-a43f-4d3f-b1ae-f4e57da5f55f.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:56:48,921 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (123) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/123/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/123/galaxy_123.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:48,934 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 123 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:48,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 123 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:49,271 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:56:58,399 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-wc9bb with k8s id: gxy-wc9bb succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:56:58,533 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 123: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:57:05,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 123 finished +galaxy.model.metadata DEBUG 2024-09-03 06:57:05,433 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 147 +galaxy.jobs INFO 2024-09-03 06:57:05,464 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 123 in /galaxy/server/database/jobs_directory/000/123 +galaxy.jobs DEBUG 2024-09-03 06:57:05,512 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 123 executed (101.334 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:05,524 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 123 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:57:06,087 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 124 +tpv.core.entities DEBUG 2024-09-03 06:57:06,110 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:57:06,111 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:57:06,115 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:57:06,123 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:57:06,135 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Working directory for job is: /galaxy/server/database/jobs_directory/000/124 +galaxy.jobs.runners DEBUG 2024-09-03 06:57:06,143 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [124] queued (27.863 ms) +galaxy.jobs.handler INFO 2024-09-03 06:57:06,144 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:06,146 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 124 +galaxy.jobs DEBUG 2024-09-03 06:57:06,217 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [124] prepared (62.587 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:57:06,217 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:57:06,217 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:57:06,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:57:06,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/124/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/124/configs/tmp1p8bg8a1' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/124/configs/tmpc_vtuxv1' -Q '/galaxy/server/database/jobs_directory/000/124/configs/tmp1p8bg8a1' --comment_char='#' -o '/galaxy/server/database/objects/5/3/5/dataset_5354a852-f6e3-4a2e-b605-fbe1325fc45f.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:57:06,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (124) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/124/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/124/galaxy_124.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:06,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 124 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:57:06,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:57:06,276 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:57:06,295 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:06,312 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 124 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:07,437 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:10,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-rnfbc with k8s id: gxy-rnfbc succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:57:10,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 124: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:57:17,609 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 124 finished +galaxy.model.metadata DEBUG 2024-09-03 06:57:17,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 148 +galaxy.jobs INFO 2024-09-03 06:57:17,679 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 124 in /galaxy/server/database/jobs_directory/000/124 +galaxy.jobs DEBUG 2024-09-03 06:57:17,722 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 124 executed (91.408 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:17,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 124 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:57:19,381 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 126, 125 +tpv.core.entities DEBUG 2024-09-03 06:57:19,405 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:57:19,406 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:57:19,409 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:57:19,419 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:57:19,430 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Working directory for job is: /galaxy/server/database/jobs_directory/000/125 +galaxy.jobs.runners DEBUG 2024-09-03 06:57:19,437 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [125] queued (27.505 ms) +galaxy.jobs.handler INFO 2024-09-03 06:57:19,440 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:19,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 125 +tpv.core.entities DEBUG 2024-09-03 06:57:19,452 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:57:19,452 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:57:19,457 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:57:19,470 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:57:19,496 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Working directory for job is: /galaxy/server/database/jobs_directory/000/126 +galaxy.jobs.runners DEBUG 2024-09-03 06:57:19,504 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [126] queued (46.904 ms) +galaxy.jobs.handler INFO 2024-09-03 06:57:19,507 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:19,509 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 126 +galaxy.jobs DEBUG 2024-09-03 06:57:19,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [125] prepared (94.988 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:57:19,571 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/125/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/125/registry.xml' '/galaxy/server/database/jobs_directory/000/125/upload_params.json' '149:/galaxy/server/database/objects/e/1/f/dataset_e1f4193a-0d03-4c43-ad07-dcbf6fff57fb_files:/galaxy/server/database/objects/e/1/f/dataset_e1f4193a-0d03-4c43-ad07-dcbf6fff57fb.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:57:19,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (125) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/125/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/125/galaxy_125.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-09-03 06:57:19,596 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [126] prepared (79.478 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:19,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 125 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:19,616 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 125 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-09-03 06:57:19,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/126/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/126/registry.xml' '/galaxy/server/database/jobs_directory/000/126/upload_params.json' '150:/galaxy/server/database/objects/b/d/c/dataset_bdc547c2-4b29-49ad-a388-035b525609aa_files:/galaxy/server/database/objects/b/d/c/dataset_bdc547c2-4b29-49ad-a388-035b525609aa.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:57:19,633 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (126) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/126/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/126/galaxy_126.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:19,649 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 126 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:19,661 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 126 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:20,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:20,558 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:29,779 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-4jk6v with k8s id: gxy-4jk6v succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:29,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-vrt8z with k8s id: gxy-vrt8z succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:57:29,911 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 125: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:57:29,930 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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 2024-09-03 06:57:37,459 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 125 finished +galaxy.model.metadata DEBUG 2024-09-03 06:57:37,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 149 +galaxy.jobs.runners DEBUG 2024-09-03 06:57:37,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 126 finished +galaxy.jobs INFO 2024-09-03 06:57:37,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 125 in /galaxy/server/database/jobs_directory/000/125 +galaxy.model.metadata DEBUG 2024-09-03 06:57:37,573 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 150 +galaxy.jobs DEBUG 2024-09-03 06:57:37,598 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 125 executed (118.085 ms) +galaxy.jobs INFO 2024-09-03 06:57:37,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 126 in /galaxy/server/database/jobs_directory/000/126 +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:37,613 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 125 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs DEBUG 2024-09-03 06:57:37,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 126 executed (111.981 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:37,684 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 126 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:57:37,996 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 127 +tpv.core.entities DEBUG 2024-09-03 06:57:38,025 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:57:38,025 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:57:38,029 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:57:38,041 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:57:38,056 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Working directory for job is: /galaxy/server/database/jobs_directory/000/127 +galaxy.jobs.runners DEBUG 2024-09-03 06:57:38,065 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [127] queued (35.810 ms) +galaxy.jobs.handler INFO 2024-09-03 06:57:38,068 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:38,070 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 127 +galaxy.jobs DEBUG 2024-09-03 06:57:38,141 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [127] prepared (64.735 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:57:38,141 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:57:38,142 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:57:38,164 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:57:38,185 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/127/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/127/configs/tmpkeuieg92' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/127/configs/tmpxwc4bz9w' -Q '/galaxy/server/database/jobs_directory/000/127/configs/tmpkeuieg92' --comment_char='#' -o '/galaxy/server/database/objects/9/2/6/dataset_926758ac-b26e-4c97-9032-d068c0fdcf03.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:57:38,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (127) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/127/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/127/galaxy_127.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:38,208 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 127 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:57:38,209 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:57:38,209 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:57:38,229 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:38,244 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 127 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:38,826 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:42,890 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-4ngrt with k8s id: gxy-4ngrt succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:57:43,013 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 127: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:57:50,072 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 127 finished +galaxy.model.metadata DEBUG 2024-09-03 06:57:50,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 151 +galaxy.jobs INFO 2024-09-03 06:57:50,150 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 127 in /galaxy/server/database/jobs_directory/000/127 +galaxy.jobs DEBUG 2024-09-03 06:57:50,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 127 executed (101.666 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:50,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 127 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:57:51,284 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 128 +tpv.core.entities DEBUG 2024-09-03 06:57:51,312 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:57:51,312 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:57:51,316 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:57:51,329 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:57:51,343 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Working directory for job is: /galaxy/server/database/jobs_directory/000/128 +galaxy.jobs.runners DEBUG 2024-09-03 06:57:51,349 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [128] queued (32.827 ms) +galaxy.jobs.handler INFO 2024-09-03 06:57:51,352 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:51,354 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 128 +galaxy.jobs DEBUG 2024-09-03 06:57:51,433 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [128] prepared (69.082 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:57:51,452 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/128/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/128/registry.xml' '/galaxy/server/database/jobs_directory/000/128/upload_params.json' '152:/galaxy/server/database/objects/e/1/0/dataset_e106e609-955c-4b07-8741-017cc91a020e_files:/galaxy/server/database/objects/e/1/0/dataset_e106e609-955c-4b07-8741-017cc91a020e.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:57:51,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (128) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/128/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/128/galaxy_128.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:51,476 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 128 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:51,489 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 128 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:51,915 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-09-03 06:57:52,355 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 129 +tpv.core.entities DEBUG 2024-09-03 06:57:52,382 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:57:52,382 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:57:52,386 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:57:52,397 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:57:52,412 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Working directory for job is: /galaxy/server/database/jobs_directory/000/129 +galaxy.jobs.runners DEBUG 2024-09-03 06:57:52,419 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [129] queued (32.382 ms) +galaxy.jobs.handler INFO 2024-09-03 06:57:52,421 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (129) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:52,423 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 129 +galaxy.jobs DEBUG 2024-09-03 06:57:52,509 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [129] prepared (77.515 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:57:52,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '153:/galaxy/server/database/objects/b/7/4/dataset_b746cd5b-f442-4c12-9a2d-08f780790990_files:/galaxy/server/database/objects/b/7/4/dataset_b746cd5b-f442-4c12-9a2d-08f780790990.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:57:52,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (129) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/129/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/129/galaxy_129.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:52,554 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 129 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:52,565 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 129 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:57:53,094 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:01,286 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-f8gfp with k8s id: gxy-f8gfp succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:58:01,410 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 128: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.kubernetes DEBUG 2024-09-03 06:58:02,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-rslx5 with k8s id: gxy-rslx5 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:58:02,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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 2024-09-03 06:58:08,936 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 128 finished +galaxy.model.metadata DEBUG 2024-09-03 06:58:08,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 152 +galaxy.jobs INFO 2024-09-03 06:58:09,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 128 in /galaxy/server/database/jobs_directory/000/128 +galaxy.jobs DEBUG 2024-09-03 06:58:09,053 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 128 executed (100.957 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:09,068 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 128 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-09-03 06:58:09,981 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 129 finished +galaxy.model.metadata DEBUG 2024-09-03 06:58:10,022 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 153 +galaxy.jobs INFO 2024-09-03 06:58:10,051 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 129 in /galaxy/server/database/jobs_directory/000/129 +galaxy.jobs DEBUG 2024-09-03 06:58:10,097 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 129 executed (96.483 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:10,108 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 129 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:58:10,752 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 130 +tpv.core.entities DEBUG 2024-09-03 06:58:10,781 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:58:10,781 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:58:10,784 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:58:10,792 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:58:10,805 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Working directory for job is: /galaxy/server/database/jobs_directory/000/130 +galaxy.jobs.runners DEBUG 2024-09-03 06:58:10,812 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [130] queued (27.791 ms) +galaxy.jobs.handler INFO 2024-09-03 06:58:10,814 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (130) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:10,816 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 130 +galaxy.jobs DEBUG 2024-09-03 06:58:10,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [130] prepared (63.851 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:58:10,888 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:58:10,888 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:58:10,911 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:58:10,930 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/130/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/130/configs/tmp7_jrxnls' && cp '/galaxy/server/database/objects/e/1/0/dataset_e106e609-955c-4b07-8741-017cc91a020e.dat' 'workdb.sqlite' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/130/configs/tmpy5o6f8gl' -Q '/galaxy/server/database/jobs_directory/000/130/configs/tmp7_jrxnls' --comment_char='#' -o '/galaxy/server/database/objects/8/c/8/dataset_8c882cff-dcfc-4326-b285-ddc57cecc7db.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:58:10,938 [pN:job_handler_0,p:8,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.kubernetes DEBUG 2024-09-03 06:58:10,950 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 130 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:58:10,950 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:58:10,951 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:58:10,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:10,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 130 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:11,389 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:14,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-44j2j failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:14,457 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:14,493 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-44j2j. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:14,501 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 130 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-09-03 06:58:14,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-09-03-06-11-1/jobs/gxy-44j2j + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-44j2j": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:14,534 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:14,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (130/gxy-44j2j) tool_stdout: +SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name + +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:14,541 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (130/gxy-44j2j) tool_stderr: JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/b/7/4/dataset_b746cd5b-f442-4c12-9a2d-08f780790990.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\d+)/(\\d+)/(\\d+)', 'replace': '19\\3-\\2-\\1'}]}]} + +SQL: +SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name + +rowcount: None + +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:14,541 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (130/gxy-44j2j) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:14,541 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (130/gxy-44j2j) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-44j2j. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:14,541 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Attempting to stop job 130 (gxy-44j2j) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:14,549 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Found job with id gxy-44j2j to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:14,550 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 130 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:14,609 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (130/gxy-44j2j) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-09-03 06:58:15,882 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 131 +tpv.core.entities DEBUG 2024-09-03 06:58:15,904 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:58:15,905 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:58:15,908 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:58:15,916 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:58:15,928 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Working directory for job is: /galaxy/server/database/jobs_directory/000/131 +galaxy.jobs.runners DEBUG 2024-09-03 06:58:15,934 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [131] queued (26.706 ms) +galaxy.jobs.handler INFO 2024-09-03 06:58:15,937 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (131) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:15,939 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 131 +galaxy.jobs DEBUG 2024-09-03 06:58:16,016 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [131] prepared (68.728 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:58:16,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/131/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/131/registry.xml' '/galaxy/server/database/jobs_directory/000/131/upload_params.json' '155:/galaxy/server/database/objects/f/8/d/dataset_f8d22288-095a-4cc8-9820-aba8c04285dc_files:/galaxy/server/database/objects/f/8/d/dataset_f8d22288-095a-4cc8-9820-aba8c04285dc.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:58:16,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (131) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/131/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/131/galaxy_131.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:16,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 131 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:16,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 131 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:16,549 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:25,675 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-2p8qh with k8s id: gxy-2p8qh succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:58:25,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 131: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 06:58:32,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 131 finished +galaxy.model.metadata DEBUG 2024-09-03 06:58:32,710 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 155 +galaxy.jobs INFO 2024-09-03 06:58:32,742 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 131 in /galaxy/server/database/jobs_directory/000/131 +galaxy.jobs DEBUG 2024-09-03 06:58:32,796 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 131 executed (110.326 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:32,809 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 131 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:58:33,216 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 132 +tpv.core.entities DEBUG 2024-09-03 06:58:33,243 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:58:33,244 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:58:33,247 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:58:33,256 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:58:33,269 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Working directory for job is: /galaxy/server/database/jobs_directory/000/132 +galaxy.jobs.runners DEBUG 2024-09-03 06:58:33,277 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [132] queued (30.312 ms) +galaxy.jobs.handler INFO 2024-09-03 06:58:33,279 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (132) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:33,281 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 132 +galaxy.jobs DEBUG 2024-09-03 06:58:33,352 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [132] prepared (62.925 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:58:33,352 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:58:33,352 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:58:33,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:58:33,396 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/132/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/132/configs/tmp0bod44n5' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/132/configs/tmpgwhf4d0r' -Q '/galaxy/server/database/jobs_directory/000/132/configs/tmp0bod44n5' --comment_char='#' -o '/galaxy/server/database/objects/5/c/6/dataset_5c6eb3d3-f175-46cd-b7ea-c4010a5ec942.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:58:33,405 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (132) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/132/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/132/galaxy_132.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:33,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 132 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:58:33,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:58:33,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:58:33,437 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:33,453 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 132 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:33,730 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:37,798 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-7p4kk with k8s id: gxy-7p4kk succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:58:37,926 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 132: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:58:44,736 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 132 finished +galaxy.model.metadata DEBUG 2024-09-03 06:58:44,780 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 156 +galaxy.jobs INFO 2024-09-03 06:58:44,816 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 132 in /galaxy/server/database/jobs_directory/000/132 +galaxy.jobs DEBUG 2024-09-03 06:58:44,861 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 132 executed (105.881 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:44,874 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 132 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:58:46,479 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 133 +tpv.core.entities DEBUG 2024-09-03 06:58:46,504 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:58:46,505 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:58:46,509 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:58:46,520 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:58:46,532 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Working directory for job is: /galaxy/server/database/jobs_directory/000/133 +galaxy.jobs.runners DEBUG 2024-09-03 06:58:46,538 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [133] queued (29.103 ms) +galaxy.jobs.handler INFO 2024-09-03 06:58:46,540 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (133) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:46,542 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 133 +galaxy.jobs DEBUG 2024-09-03 06:58:46,624 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [133] prepared (75.206 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:58:46,642 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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' '157:/galaxy/server/database/objects/f/e/5/dataset_fe5df193-4c7d-48cd-8f66-680bb6efd073_files:/galaxy/server/database/objects/f/e/5/dataset_fe5df193-4c7d-48cd-8f66-680bb6efd073.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:58:46,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (133) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/133/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/133/galaxy_133.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:46,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 133 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:46,674 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 133 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:46,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:58:56,071 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-wxxjb with k8s id: gxy-wxxjb succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:58:56,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 133: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:59:03,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 133 finished +galaxy.model.metadata DEBUG 2024-09-03 06:59:03,293 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 157 +galaxy.jobs INFO 2024-09-03 06:59:03,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 133 in /galaxy/server/database/jobs_directory/000/133 +galaxy.jobs DEBUG 2024-09-03 06:59:03,380 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 133 executed (113.255 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:03,394 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 133 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:59:03,820 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 134 +tpv.core.entities DEBUG 2024-09-03 06:59:03,846 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:59:03,847 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:59:03,850 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:59:03,860 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:59:03,873 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Working directory for job is: /galaxy/server/database/jobs_directory/000/134 +galaxy.jobs.runners DEBUG 2024-09-03 06:59:03,882 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [134] queued (31.456 ms) +galaxy.jobs.handler INFO 2024-09-03 06:59:03,884 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (134) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:03,886 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 134 +galaxy.jobs DEBUG 2024-09-03 06:59:03,960 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [134] prepared (65.671 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:59:03,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:59:03,961 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:59:04,174 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:59:04,196 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/134/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/134/configs/tmpi69szrgb' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/134/configs/tmpgpj8q8gd' -Q '/galaxy/server/database/jobs_directory/000/134/configs/tmpi69szrgb' -o '/galaxy/server/database/objects/c/e/3/dataset_ce39e522-d6d1-4fb7-b7d6-8f39c5bbb3b3.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:59:04,207 [pN:job_handler_0,p:8,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; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:04,223 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 134 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:59:04,223 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:59:04,223 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:59:04,246 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:04,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 134 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:05,102 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:09,231 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-xvfnk with k8s id: gxy-xvfnk succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:59:09,360 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 134: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:59:16,448 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 134 finished +galaxy.model.metadata DEBUG 2024-09-03 06:59:16,487 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 158 +galaxy.jobs INFO 2024-09-03 06:59:16,515 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 134 in /galaxy/server/database/jobs_directory/000/134 +galaxy.jobs DEBUG 2024-09-03 06:59:16,558 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 134 executed (91.010 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:16,577 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 134 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:59:18,192 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 135 +tpv.core.entities DEBUG 2024-09-03 06:59:18,221 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:59:18,221 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:59:18,225 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:59:18,236 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:59:18,250 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Working directory for job is: /galaxy/server/database/jobs_directory/000/135 +galaxy.jobs.runners DEBUG 2024-09-03 06:59:18,257 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [135] queued (31.621 ms) +galaxy.jobs.handler INFO 2024-09-03 06:59:18,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (135) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:18,262 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 135 +galaxy.jobs DEBUG 2024-09-03 06:59:18,353 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [135] prepared (82.797 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:59:18,373 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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' '159:/galaxy/server/database/objects/0/6/7/dataset_067f95a7-2059-4664-b6d2-3a092ef4cc7c_files:/galaxy/server/database/objects/0/6/7/dataset_067f95a7-2059-4664-b6d2-3a092ef4cc7c.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:59:18,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (135) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/135/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/135/galaxy_135.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:18,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 135 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:18,413 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 135 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:19,258 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:27,408 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-hcrpq failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:27,408 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:27,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-hcrpq. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:27,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 135 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-09-03 06:59:27,464 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-09-03-06-11-1/jobs/gxy-hcrpq + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-hcrpq": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:27,473 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:27,480 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (135/gxy-hcrpq) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:27,480 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (135/gxy-hcrpq) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:27,480 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (135/gxy-hcrpq) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:27,480 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (135/gxy-hcrpq) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-hcrpq. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:27,480 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Attempting to stop job 135 (gxy-hcrpq) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:27,488 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Found job with id gxy-hcrpq to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:27,490 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 135 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:27,547 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (135/gxy-hcrpq) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-09-03 06:59:28,437 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 136 +tpv.core.entities DEBUG 2024-09-03 06:59:28,461 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:59:28,461 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:59:28,464 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:59:28,473 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:59:28,484 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Working directory for job is: /galaxy/server/database/jobs_directory/000/136 +galaxy.jobs.runners DEBUG 2024-09-03 06:59:28,491 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [136] queued (26.555 ms) +galaxy.jobs.handler INFO 2024-09-03 06:59:28,493 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (136) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:28,496 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 136 +galaxy.jobs DEBUG 2024-09-03 06:59:28,572 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [136] prepared (69.468 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:59:28,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '160:/galaxy/server/database/objects/0/6/d/dataset_06d6bda3-00a4-44af-bf95-4105b34dca77_files:/galaxy/server/database/objects/0/6/d/dataset_06d6bda3-00a4-44af-bf95-4105b34dca77.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:59:28,604 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (136) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/136/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/136/galaxy_136.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:28,620 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 136 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:28,637 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 136 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:29,489 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:37,623 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ddswn with k8s id: gxy-ddswn succeeded +galaxy.jobs.runners DEBUG 2024-09-03 06:59:37,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 136: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 06:59:44,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 136 finished +galaxy.model.metadata DEBUG 2024-09-03 06:59:44,730 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 160 +galaxy.jobs INFO 2024-09-03 06:59:44,760 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 136 in /galaxy/server/database/jobs_directory/000/136 +galaxy.jobs DEBUG 2024-09-03 06:59:44,815 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 136 executed (108.574 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:44,825 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 136 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 06:59:45,791 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 137 +tpv.core.entities DEBUG 2024-09-03 06:59:45,816 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:59:45,817 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:59:45,820 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:59:45,830 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:59:45,845 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Working directory for job is: /galaxy/server/database/jobs_directory/000/137 +galaxy.jobs.runners DEBUG 2024-09-03 06:59:45,855 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [137] queued (34.603 ms) +galaxy.jobs.handler INFO 2024-09-03 06:59:45,857 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (137) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:45,859 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 137 +galaxy.jobs DEBUG 2024-09-03 06:59:45,931 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [137] prepared (65.208 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 06:59:45,931 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:59:45,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:59:45,955 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 06:59:45,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/137/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/137/configs/tmpljwbu6nc' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/137/configs/tmpmsqj69lx' -Q '/galaxy/server/database/jobs_directory/000/137/configs/tmpljwbu6nc' --comment_char='#' -o '/galaxy/server/database/objects/6/0/d/dataset_60da0121-d131-4f09-8906-54a9df5c81a7.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:59:45,994 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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; +if [ -f "/galaxy/server/database/jobs_directory/000/137/working/results0.tsv" -a -f "/galaxy/server/database/objects/a/f/5/dataset_af560828-98a1-4e90-a79c-bb812ced1a2b.dat" ] ; then cp "/galaxy/server/database/jobs_directory/000/137/working/results0.tsv" "/galaxy/server/database/objects/a/f/5/dataset_af560828-98a1-4e90-a79c-bb812ced1a2b.dat" ; fi; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:46,008 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 137 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 06:59:46,008 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 06:59:46,008 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 06:59:46,030 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:46,047 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 137 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:46,645 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:49,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-mpbcg failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:49,710 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:49,750 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-mpbcg. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:49,761 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 137 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes ERROR 2024-09-03 06:59:49,786 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-09-03-06-11-1/jobs/gxy-mpbcg + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-mpbcg": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:49,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:49,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (137/gxy-mpbcg) tool_stdout: +SELECT scan,"m/z", "Precursor m/z Error [ppm]", Sequence, "Protein(s)", confidence FROM PSMs WHERE NOT re_search(', ',"Protein(s)") + +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:49,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (137/gxy-mpbcg) tool_stderr: JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/0/6/d/dataset_06d6bda3-00a4-44af-bf95-4105b34dca77.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'scan,,,,,,confidence', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19, 23]}]}], 'sql_stmts': ['UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0'], 'queries': [{'query': 'SELECT * FROM psms WHERE confidence > 97.0', 'result_file': 'results0.tsv', 'header': ''}]} + +DB modification: UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0 +rowcount: + +SQL: SELECT * FROM psms WHERE confidence > 97.0 +rowcount: None + +SQL: +SELECT scan,"m/z", "Precursor m/z Error [ppm]", Sequence, "Protein(s)", confidence FROM PSMs WHERE NOT re_search(', ',"Protein(s)") + +rowcount: None + +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:49,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (137/gxy-mpbcg) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:49,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (137/gxy-mpbcg) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-mpbcg. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:49,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Attempting to stop job 137 (gxy-mpbcg) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:49,806 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Found job with id gxy-mpbcg to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:49,808 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 137 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:49,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (137/gxy-mpbcg) Terminated at user's request +galaxy.util WARNING 2024-09-03 06:59:49,890 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/a/f/5/dataset_af560828-98a1-4e90-a79c-bb812ced1a2b.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/a/f/5/dataset_af560828-98a1-4e90-a79c-bb812ced1a2b.dat' +galaxy.jobs.handler DEBUG 2024-09-03 06:59:50,930 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 138 +tpv.core.entities DEBUG 2024-09-03 06:59:50,949 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 06:59:50,949 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 06:59:50,952 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 06:59:50,960 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 06:59:50,972 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Working directory for job is: /galaxy/server/database/jobs_directory/000/138 +galaxy.jobs.runners DEBUG 2024-09-03 06:59:50,978 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [138] queued (26.345 ms) +galaxy.jobs.handler INFO 2024-09-03 06:59:50,981 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (138) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:50,983 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 138 +galaxy.jobs DEBUG 2024-09-03 06:59:51,055 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [138] prepared (64.302 ms) +galaxy.jobs.command_factory INFO 2024-09-03 06:59:51,072 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/138/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/138/registry.xml' '/galaxy/server/database/jobs_directory/000/138/upload_params.json' '163:/galaxy/server/database/objects/1/7/2/dataset_17264408-078a-4185-b36d-8847c64e8338_files:/galaxy/server/database/objects/1/7/2/dataset_17264408-078a-4185-b36d-8847c64e8338.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 06:59:51,081 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (138) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/138/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/138/galaxy_138.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:51,093 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 138 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:51,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 138 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 06:59:51,806 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:01,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-dq599 with k8s id: gxy-dq599 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:00:01,152 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 138: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 07:00:08,321 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 138 finished +galaxy.model.metadata DEBUG 2024-09-03 07:00:08,366 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 163 +galaxy.jobs INFO 2024-09-03 07:00:08,402 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 138 in /galaxy/server/database/jobs_directory/000/138 +galaxy.jobs DEBUG 2024-09-03 07:00:08,445 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 138 executed (102.675 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:08,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 138 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:00:09,280 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 139 +tpv.core.entities DEBUG 2024-09-03 07:00:09,306 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:00:09,306 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:00:09,310 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:00:09,322 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:00:09,338 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Working directory for job is: /galaxy/server/database/jobs_directory/000/139 +galaxy.jobs.runners DEBUG 2024-09-03 07:00:09,346 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [139] queued (36.343 ms) +galaxy.jobs.handler INFO 2024-09-03 07:00:09,348 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (139) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:09,351 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 139 +galaxy.jobs DEBUG 2024-09-03 07:00:09,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [139] prepared (62.716 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 07:00:09,421 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:00:09,421 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:00:09,441 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 07:00:09,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/139/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/139/configs/tmp2i9s9xas' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/139/configs/tmp_r877wgp' -Q '/galaxy/server/database/jobs_directory/000/139/configs/tmp2i9s9xas' -o '/galaxy/server/database/objects/4/3/6/dataset_436c83b1-570a-44d6-9780-e6bbc572a3d3.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:00:09,470 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (139) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/139/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/139/galaxy_139.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:09,485 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 139 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 07:00:09,485 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:00:09,485 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:00:09,504 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:09,520 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 139 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:10,047 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:14,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-9vs5k with k8s id: gxy-9vs5k succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:00:14,264 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 139: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 07:00:21,442 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 139 finished +galaxy.model.metadata DEBUG 2024-09-03 07:00:21,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 164 +galaxy.jobs INFO 2024-09-03 07:00:21,517 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 139 in /galaxy/server/database/jobs_directory/000/139 +galaxy.jobs DEBUG 2024-09-03 07:00:21,570 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 139 executed (108.857 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:21,584 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 139 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:00:22,564 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 140 +tpv.core.entities DEBUG 2024-09-03 07:00:22,587 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:00:22,587 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:00:22,591 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:00:22,601 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:00:22,613 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Working directory for job is: /galaxy/server/database/jobs_directory/000/140 +galaxy.jobs.runners DEBUG 2024-09-03 07:00:22,620 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [140] queued (29.549 ms) +galaxy.jobs.handler INFO 2024-09-03 07:00:22,623 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (140) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:22,625 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 140 +galaxy.jobs DEBUG 2024-09-03 07:00:22,715 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [140] prepared (82.413 ms) +galaxy.jobs.command_factory INFO 2024-09-03 07:00:22,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/140/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/140/registry.xml' '/galaxy/server/database/jobs_directory/000/140/upload_params.json' '165:/galaxy/server/database/objects/b/b/f/dataset_bbfd3edd-633e-453b-8844-0557916a7273_files:/galaxy/server/database/objects/b/b/f/dataset_bbfd3edd-633e-453b-8844-0557916a7273.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:00:22,744 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:22,758 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 140 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:22,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 140 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:23,177 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:32,299 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-zgr5w with k8s id: gxy-zgr5w succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:00:32,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 140: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 07:00:39,495 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 140 finished +galaxy.model.metadata DEBUG 2024-09-03 07:00:39,541 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 165 +galaxy.jobs INFO 2024-09-03 07:00:39,576 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 140 in /galaxy/server/database/jobs_directory/000/140 +galaxy.jobs DEBUG 2024-09-03 07:00:39,634 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 140 executed (118.001 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:39,647 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 140 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:00:40,948 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 141 +tpv.core.entities DEBUG 2024-09-03 07:00:40,972 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:00:40,973 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:00:40,976 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:00:40,986 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:00:40,999 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Working directory for job is: /galaxy/server/database/jobs_directory/000/141 +galaxy.jobs.runners DEBUG 2024-09-03 07:00:41,007 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [141] queued (30.435 ms) +galaxy.jobs.handler INFO 2024-09-03 07:00:41,009 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (141) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:41,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 141 +galaxy.jobs DEBUG 2024-09-03 07:00:41,075 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [141] prepared (57.559 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 07:00:41,075 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:00:41,076 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:00:41,096 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 07:00:41,116 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/141/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/141/configs/tmp8gv777h3' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/141/configs/tmp7zy_0vob' -Q '/galaxy/server/database/jobs_directory/000/141/configs/tmp8gv777h3' -o '/galaxy/server/database/objects/6/d/5/dataset_6d52d198-b4fa-4473-93eb-04bc9b64d44f.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:00:41,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (141) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/141/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/141/galaxy_141.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:41,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 141 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 07:00:41,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:00:41,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:00:41,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:41,178 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 141 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:41,326 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:45,385 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-rd7rk with k8s id: gxy-rd7rk succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:00:45,517 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 141: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 07:00:52,583 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 141 finished +galaxy.model.metadata DEBUG 2024-09-03 07:00:52,630 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 166 +galaxy.jobs INFO 2024-09-03 07:00:52,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 141 in /galaxy/server/database/jobs_directory/000/141 +galaxy.jobs DEBUG 2024-09-03 07:00:52,712 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 141 executed (107.665 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:52,897 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 141 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:00:54,224 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 142 +tpv.core.entities DEBUG 2024-09-03 07:00:54,246 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:00:54,246 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:00:54,249 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:00:54,261 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:00:54,275 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Working directory for job is: /galaxy/server/database/jobs_directory/000/142 +galaxy.jobs.runners DEBUG 2024-09-03 07:00:54,283 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [142] queued (33.655 ms) +galaxy.jobs.handler INFO 2024-09-03 07:00:54,285 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (142) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:54,287 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 142 +galaxy.jobs DEBUG 2024-09-03 07:00:54,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [142] prepared (83.425 ms) +galaxy.jobs.command_factory INFO 2024-09-03 07:00:54,403 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/142/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/142/registry.xml' '/galaxy/server/database/jobs_directory/000/142/upload_params.json' '167:/galaxy/server/database/objects/a/d/b/dataset_adb7bbec-6945-4a3b-8861-e7b2879da4c8_files:/galaxy/server/database/objects/a/d/b/dataset_adb7bbec-6945-4a3b-8861-e7b2879da4c8.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:00:54,412 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (142) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/142/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/142/galaxy_142.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:54,425 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 142 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:54,439 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 142 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:00:55,410 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:04,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-9nbbt with k8s id: gxy-9nbbt succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:01:04,657 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 142: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 07:01:11,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 142 finished +galaxy.model.metadata DEBUG 2024-09-03 07:01:11,889 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 167 +galaxy.jobs INFO 2024-09-03 07:01:11,926 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 142 in /galaxy/server/database/jobs_directory/000/142 +galaxy.jobs DEBUG 2024-09-03 07:01:11,975 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 142 executed (112.205 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:11,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 142 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:01:12,576 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 143 +tpv.core.entities DEBUG 2024-09-03 07:01:12,605 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:01:12,606 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:01:12,610 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:01:12,625 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:01:12,639 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Working directory for job is: /galaxy/server/database/jobs_directory/000/143 +galaxy.jobs.runners DEBUG 2024-09-03 07:01:12,646 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [143] queued (35.655 ms) +galaxy.jobs.handler INFO 2024-09-03 07:01:12,648 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (143) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:12,651 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 143 +galaxy.jobs DEBUG 2024-09-03 07:01:12,720 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [143] prepared (61.924 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 07:01:12,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:01:12,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:01:12,748 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 07:01:12,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/143/tool_script.sh] for tool command [cat '/galaxy/server/database/jobs_directory/000/143/configs/tmpddpl87a4' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/143/configs/tmpzdi21_fw' -Q '/galaxy/server/database/jobs_directory/000/143/configs/tmpddpl87a4' --comment_char='#' -o '/galaxy/server/database/objects/c/2/e/dataset_c2ee71db-d54d-401c-a0af-fac28dc6e34c.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:01:12,780 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (143) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/143/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/143/galaxy_143.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:12,795 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 143 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 07:01:12,795 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:01:12,795 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0: python:3.7 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:01:12,818 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/python:3.7--1,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:12,833 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 143 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:13,557 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:17,626 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-7c7qm with k8s id: gxy-7c7qm succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:01:17,760 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 143: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 07:01:24,741 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 143 finished +galaxy.model.metadata DEBUG 2024-09-03 07:01:24,782 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 168 +galaxy.jobs INFO 2024-09-03 07:01:24,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 143 in /galaxy/server/database/jobs_directory/000/143 +galaxy.jobs DEBUG 2024-09-03 07:01:24,871 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 143 executed (109.472 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:24,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 143 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:01:26,887 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 144 +tpv.core.entities DEBUG 2024-09-03 07:01:26,909 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:01:26,909 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:01:26,914 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:01:26,923 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:01:26,935 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Working directory for job is: /galaxy/server/database/jobs_directory/000/144 +galaxy.jobs.runners DEBUG 2024-09-03 07:01:26,942 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [144] queued (27.861 ms) +galaxy.jobs.handler INFO 2024-09-03 07:01:26,945 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (144) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:26,948 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 144 +galaxy.jobs DEBUG 2024-09-03 07:01:27,038 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [144] prepared (81.259 ms) +galaxy.jobs.command_factory INFO 2024-09-03 07:01:27,059 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '169:/galaxy/server/database/objects/2/d/8/dataset_2d8defe6-9a1c-41a8-829c-4c9de99a08cc_files:/galaxy/server/database/objects/2/d/8/dataset_2d8defe6-9a1c-41a8-829c-4c9de99a08cc.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:01:27,068 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (144) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/144/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/144/galaxy_144.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:27,084 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 144 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:27,098 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 144 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:27,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:36,763 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-d4nsz with k8s id: gxy-d4nsz succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:01:36,903 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 144: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.runners DEBUG 2024-09-03 07:01:43,967 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 144 finished +galaxy.model.metadata DEBUG 2024-09-03 07:01:44,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 169 +galaxy.jobs INFO 2024-09-03 07:01:44,039 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 144 in /galaxy/server/database/jobs_directory/000/144 +galaxy.jobs DEBUG 2024-09-03 07:01:44,094 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 144 executed (107.527 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:44,108 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 144 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:01:45,232 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 145 +tpv.core.entities DEBUG 2024-09-03 07:01:45,256 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:01:45,257 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:01:45,262 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:01:45,272 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:01:45,285 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Working directory for job is: /galaxy/server/database/jobs_directory/000/145 +galaxy.jobs.runners DEBUG 2024-09-03 07:01:45,293 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [145] queued (30.851 ms) +galaxy.jobs.handler INFO 2024-09-03 07:01:45,295 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (145) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:45,298 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 145 +galaxy.jobs DEBUG 2024-09-03 07:01:45,356 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [145] prepared (48.293 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 07:01:45,357 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:01:45,357 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1: mulled-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:01:45,550 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 07:01:45,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/145/tool_script.sh] for tool command [python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/372967836e98/column_remove_by_header/column_remove_by_header.py' '/galaxy/server/database/objects/2/d/8/dataset_2d8defe6-9a1c-41a8-829c-4c9de99a08cc.dat' '/galaxy/server/database/objects/d/3/b/dataset_d3bda304-115e-4a00-a497-1d448cdbbdb7.dat' ' ' '' '#' 'a'] +galaxy.jobs.runners DEBUG 2024-09-03 07:01:45,595 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:45,612 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 145 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 07:01:45,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:01:45,619 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1: mulled-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:01:45,639 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:45,670 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 145 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:45,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:01:55,041 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-pgtzf with k8s id: gxy-pgtzf succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:01:55,172 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 145: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 07:02:02,114 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 145 finished +galaxy.model.metadata DEBUG 2024-09-03 07:02:02,161 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 170 +galaxy.jobs INFO 2024-09-03 07:02:02,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 145 in /galaxy/server/database/jobs_directory/000/145 +galaxy.jobs DEBUG 2024-09-03 07:02:02,244 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 145 executed (106.901 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:02,256 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 145 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:02:03,594 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 146 +tpv.core.entities DEBUG 2024-09-03 07:02:03,618 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:02:03,619 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:02:03,622 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:02:03,631 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:02:03,643 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Working directory for job is: /galaxy/server/database/jobs_directory/000/146 +galaxy.jobs.runners DEBUG 2024-09-03 07:02:03,650 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [146] queued (27.264 ms) +galaxy.jobs.handler INFO 2024-09-03 07:02:03,652 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (146) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:03,654 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 146 +galaxy.jobs DEBUG 2024-09-03 07:02:03,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [146] prepared (73.671 ms) +galaxy.jobs.command_factory INFO 2024-09-03 07:02:03,753 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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' '171:/galaxy/server/database/objects/9/0/5/dataset_90557dec-22a2-4d49-a45c-b902d28ba311_files:/galaxy/server/database/objects/9/0/5/dataset_90557dec-22a2-4d49-a45c-b902d28ba311.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:02:03,761 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (146) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/146/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/146/galaxy_146.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:03,775 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 146 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:03,790 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 146 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:04,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:13,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-2s8sb with k8s id: gxy-2s8sb succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:02:13,342 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 146: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 07:02:20,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 146 finished +galaxy.model.metadata DEBUG 2024-09-03 07:02:20,471 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 171 +galaxy.jobs INFO 2024-09-03 07:02:20,507 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 146 in /galaxy/server/database/jobs_directory/000/146 +galaxy.jobs DEBUG 2024-09-03 07:02:20,559 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 146 executed (112.561 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:20,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 146 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:02:20,955 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 147 +tpv.core.entities DEBUG 2024-09-03 07:02:20,983 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:02:20,984 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:02:20,988 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:02:20,999 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:02:21,013 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Working directory for job is: /galaxy/server/database/jobs_directory/000/147 +galaxy.jobs.runners DEBUG 2024-09-03 07:02:21,021 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [147] queued (33.098 ms) +galaxy.jobs.handler INFO 2024-09-03 07:02:21,024 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (147) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:21,025 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 147 +galaxy.jobs DEBUG 2024-09-03 07:02:21,076 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [147] prepared (42.536 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 07:02:21,076 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:02:21,076 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1: mulled-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:02:21,103 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 07:02:21,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/147/tool_script.sh] for tool command [python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/372967836e98/column_remove_by_header/column_remove_by_header.py' '/galaxy/server/database/objects/9/0/5/dataset_90557dec-22a2-4d49-a45c-b902d28ba311.dat' '/galaxy/server/database/objects/b/9/2/dataset_b923e770-5fe7-4f3c-a82a-2e585fb02633.dat' ' ' '--keep' '#' 'KEY' 'a'] +galaxy.jobs.runners DEBUG 2024-09-03 07:02:21,138 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (147) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/147/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/147/galaxy_147.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:21,154 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 147 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 07:02:21,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:02:21,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1: mulled-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:02:21,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-975985c5f84877700b556bc77586e7e90986b693:e6883c0cde219a11f5cd7b8a2577fde5fc086eb2-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:21,206 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 147 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:22,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:25,290 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-9dwlv with k8s id: gxy-9dwlv succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:02:25,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 147: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 07:02:32,520 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 147 finished +galaxy.model.metadata DEBUG 2024-09-03 07:02:32,564 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 172 +galaxy.jobs INFO 2024-09-03 07:02:32,599 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 147 in /galaxy/server/database/jobs_directory/000/147 +galaxy.jobs DEBUG 2024-09-03 07:02:32,646 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 147 executed (105.342 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:32,658 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 147 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:02:35,403 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 148 +tpv.core.entities DEBUG 2024-09-03 07:02:35,431 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:02:35,431 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:02:35,435 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:02:35,447 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:02:35,465 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Working directory for job is: /galaxy/server/database/jobs_directory/000/148 +galaxy.jobs.runners DEBUG 2024-09-03 07:02:35,473 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [148] queued (38.056 ms) +galaxy.jobs.handler INFO 2024-09-03 07:02:35,475 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (148) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:35,478 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 148 +galaxy.jobs DEBUG 2024-09-03 07:02:35,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [148] prepared (85.583 ms) +galaxy.jobs.command_factory INFO 2024-09-03 07:02:35,596 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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' '173:/galaxy/server/database/objects/0/a/7/dataset_0a73327e-d103-4fbf-bfe1-65608e386907_files:/galaxy/server/database/objects/0/a/7/dataset_0a73327e-d103-4fbf-bfe1-65608e386907.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:02:35,606 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (148) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/148/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/148/galaxy_148.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:35,621 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 148 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:35,637 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 148 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:36,319 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:45,446 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ljt86 with k8s id: gxy-ljt86 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:02:45,568 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 148: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 07:02:52,635 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 148 finished +galaxy.model.metadata DEBUG 2024-09-03 07:02:52,679 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 173 +galaxy.jobs INFO 2024-09-03 07:02:52,711 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 148 in /galaxy/server/database/jobs_directory/000/148 +galaxy.jobs DEBUG 2024-09-03 07:02:52,760 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 148 executed (106.936 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:52,863 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 148 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:02:53,810 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 149 +tpv.core.entities DEBUG 2024-09-03 07:02:53,839 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:02:53,839 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:02:53,843 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:02:53,853 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:02:53,867 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Working directory for job is: /galaxy/server/database/jobs_directory/000/149 +galaxy.jobs.runners DEBUG 2024-09-03 07:02:53,876 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [149] queued (32.874 ms) +galaxy.jobs.handler INFO 2024-09-03 07:02:53,878 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (149) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:53,880 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 149 +galaxy.jobs DEBUG 2024-09-03 07:02:53,950 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [149] prepared (61.630 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 07:02:53,951 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:02:53,951 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:02:54,144 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 07:02:54,165 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/149/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/149/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/0/a/7/dataset_0a73327e-d103-4fbf-bfe1-65608e386907.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin mendelian --output-type 'v' input.vcf.gz --trio "NA00001,NA00002,NA00006" --delete 2> tmp_stderr > '/galaxy/server/database/objects/c/c/a/dataset_ccac2b28-fe1a-4e8e-bd2a-2ab1d64054ba.dat' && cat tmp_stderr] +galaxy.jobs.runners DEBUG 2024-09-03 07:02:54,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:54,193 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 149 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 07:02:54,193 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:02:54,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:02:54,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:54,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 149 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:02:54,473 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:03,602 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-zll6z with k8s id: gxy-zll6z succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:03:03,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 149: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 07:03:10,846 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 149 finished +galaxy.model.metadata DEBUG 2024-09-03 07:03:10,914 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 174 +galaxy.jobs INFO 2024-09-03 07:03:10,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 149 in /galaxy/server/database/jobs_directory/000/149 +galaxy.jobs DEBUG 2024-09-03 07:03:10,994 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 149 executed (105.265 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:11,005 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 149 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:03:12,186 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 150 +tpv.core.entities DEBUG 2024-09-03 07:03:12,215 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:03:12,216 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:03:12,220 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:03:12,234 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:03:12,252 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Working directory for job is: /galaxy/server/database/jobs_directory/000/150 +galaxy.jobs.runners DEBUG 2024-09-03 07:03:12,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [150] queued (39.304 ms) +galaxy.jobs.handler INFO 2024-09-03 07:03:12,262 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (150) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:12,266 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 150 +galaxy.jobs DEBUG 2024-09-03 07:03:12,351 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [150] prepared (76.605 ms) +galaxy.jobs.command_factory INFO 2024-09-03 07:03:12,372 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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' '175:/galaxy/server/database/objects/f/2/6/dataset_f260f8ca-456c-4206-a345-aa84958fbc31_files:/galaxy/server/database/objects/f/2/6/dataset_f260f8ca-456c-4206-a345-aa84958fbc31.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:03:12,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (150) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/150/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/150/galaxy_150.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:12,394 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 150 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:12,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 150 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:12,632 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:21,747 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-q6c28 with k8s id: gxy-q6c28 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:03:21,878 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 150: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 07:03:28,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 150 finished +galaxy.model.metadata DEBUG 2024-09-03 07:03:28,954 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 175 +galaxy.jobs INFO 2024-09-03 07:03:28,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 150 in /galaxy/server/database/jobs_directory/000/150 +galaxy.jobs DEBUG 2024-09-03 07:03:29,027 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 150 executed (100.925 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:29,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 150 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:03:29,558 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 151 +tpv.core.entities DEBUG 2024-09-03 07:03:29,591 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:03:29,592 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:03:29,597 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:03:29,611 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:03:29,629 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Working directory for job is: /galaxy/server/database/jobs_directory/000/151 +galaxy.jobs.runners DEBUG 2024-09-03 07:03:29,638 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [151] queued (40.529 ms) +galaxy.jobs.handler INFO 2024-09-03 07:03:29,640 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (151) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:29,642 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 151 +galaxy.jobs DEBUG 2024-09-03 07:03:29,685 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [151] prepared (35.477 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 07:03:29,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:03:29,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:03:29,711 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 07:03:29,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/151/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/151/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/2/6/dataset_f260f8ca-456c-4206-a345-aa84958fbc31.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin mendelian --output-type 'v' input.vcf.gz --trio "NA00001,NA00002,NA00006" --list x 2> tmp_stderr > '/galaxy/server/database/objects/5/5/b/dataset_55b77024-4ea0-4deb-b6b4-fafede920fb6.dat' && cat tmp_stderr] +galaxy.jobs.runners DEBUG 2024-09-03 07:03:29,749 [pN:job_handler_0,p:8,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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:29,767 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 151 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 07:03:29,775 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:03:29,775 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:03:29,796 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:0b38f50a02650e4ae53cfaa6fa2c599511f9c2c0-0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:29,815 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 151 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:30,774 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:33,825 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-pgnd2 with k8s id: gxy-pgnd2 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:03:33,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 151: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 07:03:40,945 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 151 finished +galaxy.model.metadata DEBUG 2024-09-03 07:03:40,994 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 176 +galaxy.jobs INFO 2024-09-03 07:03:41,029 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 151 in /galaxy/server/database/jobs_directory/000/151 +galaxy.jobs DEBUG 2024-09-03 07:03:41,081 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 151 executed (115.005 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:41,094 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 151 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:03:42,887 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 152 +tpv.core.entities DEBUG 2024-09-03 07:03:42,911 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:03:42,912 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:03:42,916 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:03:42,926 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:03:42,938 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Working directory for job is: /galaxy/server/database/jobs_directory/000/152 +galaxy.jobs.runners DEBUG 2024-09-03 07:03:42,945 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [152] queued (29.509 ms) +galaxy.jobs.handler INFO 2024-09-03 07:03:42,948 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (152) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:42,950 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 152 +galaxy.jobs DEBUG 2024-09-03 07:03:43,025 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [152] prepared (67.860 ms) +galaxy.jobs.command_factory INFO 2024-09-03 07:03:43,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/152/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/152/registry.xml' '/galaxy/server/database/jobs_directory/000/152/upload_params.json' '177:/galaxy/server/database/objects/d/4/d/dataset_d4dbd3f3-f2ae-40d1-b99d-541cd03c5460_files:/galaxy/server/database/objects/d/4/d/dataset_d4dbd3f3-f2ae-40d1-b99d-541cd03c5460.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:03:43,055 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (152) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/152/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/152/galaxy_152.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:43,070 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 152 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:43,084 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 152 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:43,850 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.handler DEBUG 2024-09-03 07:03:43,952 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 153, 154 +tpv.core.entities DEBUG 2024-09-03 07:03:43,976 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:03:43,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:03:43,980 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:03:43,990 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:03:44,002 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Working directory for job is: /galaxy/server/database/jobs_directory/000/153 +galaxy.jobs.runners DEBUG 2024-09-03 07:03:44,009 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [153] queued (29.240 ms) +galaxy.jobs.handler INFO 2024-09-03 07:03:44,012 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (153) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:44,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 153 +tpv.core.entities DEBUG 2024-09-03 07:03:44,026 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:03:44,027 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:03:44,031 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:03:44,045 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:03:44,072 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Working directory for job is: /galaxy/server/database/jobs_directory/000/154 +galaxy.jobs.runners DEBUG 2024-09-03 07:03:44,080 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [154] queued (49.005 ms) +galaxy.jobs.handler INFO 2024-09-03 07:03:44,083 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (154) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:44,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 154 +galaxy.jobs DEBUG 2024-09-03 07:03:44,127 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [153] prepared (98.211 ms) +galaxy.jobs.command_factory INFO 2024-09-03 07:03:44,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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' '178:/galaxy/server/database/objects/b/8/f/dataset_b8f21ecd-d4ed-424b-a20e-7ebce9969a62_files:/galaxy/server/database/objects/b/8/f/dataset_b8f21ecd-d4ed-424b-a20e-7ebce9969a62.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:03:44,164 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs DEBUG 2024-09-03 07:03:44,181 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [154] prepared (83.935 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:44,184 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 153 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:44,202 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 153 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-09-03 07:03:44,206 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/154/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/154/registry.xml' '/galaxy/server/database/jobs_directory/000/154/upload_params.json' '179:/galaxy/server/database/objects/4/a/8/dataset_4a81b91a-586b-45ac-95a1-36ddcfd6e421_files:/galaxy/server/database/objects/4/a/8/dataset_4a81b91a-586b-45ac-95a1-36ddcfd6e421.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:03:44,217 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (154) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/154/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/154/galaxy_154.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:44,235 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 154 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:44,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 154 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:44,923 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:44,973 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:53,332 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-kggw8 with k8s id: gxy-kggw8 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:53,402 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-b94px failed and it is not a deletion case. Current state: running +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:53,403 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Trying with error file in _handle_job_failure +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:53,442 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-b94px. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:53,450 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Checking if job 154 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-09-03 07:03:53,470 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 152: GALAXY_LIB="/galaxy/server/lib"; if [ "$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.kubernetes ERROR 2024-09-03 07:03:53,485 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Could not clean up k8s batch job. Ignoring... +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.12/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://34.118.224.1:443/apis/batch/v1/namespaces/edge-24-09-03-06-11-1/jobs/gxy-b94px + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 872, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 879, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 108, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.12/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-b94px": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:53,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] PP Getting into fail_job in k8s runner +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:53,505 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (154/gxy-b94px) tool_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:53,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (154/gxy-b94px) tool_stderr: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:53,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (154/gxy-b94px) job_stdout: +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:53,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (154/gxy-b94px) job_stderr: An unknown error occurred in this job and the maximum number of retries have been exceeded for job: gxy-b94px. +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:53,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Attempting to stop job 154 (gxy-b94px) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:53,513 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Found job with id gxy-b94px to delete +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:53,515 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 154 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:53,597 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (154/gxy-b94px) Terminated at user's request +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:03:54,502 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-zpdg8 with k8s id: gxy-zpdg8 succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:03:54,629 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 153: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-03 07:04:00,981 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 152 finished +galaxy.model.metadata DEBUG 2024-09-03 07:04:01,023 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 177 +galaxy.jobs INFO 2024-09-03 07:04:01,058 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 152 in /galaxy/server/database/jobs_directory/000/152 +galaxy.jobs DEBUG 2024-09-03 07:04:01,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 152 executed (104.896 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:01,117 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 152 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners DEBUG 2024-09-03 07:04:02,153 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 153 finished +galaxy.model.metadata DEBUG 2024-09-03 07:04:02,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 178 +galaxy.jobs INFO 2024-09-03 07:04:02,229 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 153 in /galaxy/server/database/jobs_directory/000/153 +galaxy.jobs DEBUG 2024-09-03 07:04:02,278 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 153 executed (106.074 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:02,290 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 153 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:04:04,421 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 155, 156 +tpv.core.entities DEBUG 2024-09-03 07:04:04,445 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:04:04,446 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:04:04,449 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:04:04,458 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:04:04,470 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Working directory for job is: /galaxy/server/database/jobs_directory/000/155 +galaxy.jobs.runners DEBUG 2024-09-03 07:04:04,476 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [155] queued (26.897 ms) +galaxy.jobs.handler INFO 2024-09-03 07:04:04,478 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (155) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:04,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 155 +tpv.core.entities DEBUG 2024-09-03 07:04:04,490 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:04:04,491 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:04:04,495 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:04:04,507 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:04:04,535 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Working directory for job is: /galaxy/server/database/jobs_directory/000/156 +galaxy.jobs.runners DEBUG 2024-09-03 07:04:04,542 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [156] queued (46.753 ms) +galaxy.jobs.handler INFO 2024-09-03 07:04:04,545 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (156) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:04,549 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 156 +galaxy.jobs DEBUG 2024-09-03 07:04:04,585 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [155] prepared (91.291 ms) +galaxy.jobs.command_factory INFO 2024-09-03 07:04:04,608 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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' '180:/galaxy/server/database/objects/1/0/4/dataset_104dbe11-503a-49b5-ab60-b2bcf328fdaf_files:/galaxy/server/database/objects/1/0/4/dataset_104dbe11-503a-49b5-ab60-b2bcf328fdaf.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:04:04,618 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs DEBUG 2024-09-03 07:04:04,632 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [156] prepared (73.338 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:04,635 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 155 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:04,647 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking if job 155 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.command_factory INFO 2024-09-03 07:04:04,653 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/156/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/156/registry.xml' '/galaxy/server/database/jobs_directory/000/156/upload_params.json' '181:/galaxy/server/database/objects/2/a/a/dataset_2aaee688-aad9-4401-b8f5-54a8cca3d4e0_files:/galaxy/server/database/objects/2/a/a/dataset_2aaee688-aad9-4401-b8f5-54a8cca3d4e0.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:04:04,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (156) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:04,677 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 156 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:04,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 156 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:05,535 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:05,581 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:13,759 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-6ggj2 with k8s id: gxy-6ggj2 succeeded +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:13,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-9mzpz with k8s id: gxy-9mzpz succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:04:13,898 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 155: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 07:04:13,926 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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 2024-09-03 07:04:21,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 156 finished +galaxy.model.metadata DEBUG 2024-09-03 07:04:21,269 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 181 +galaxy.jobs.runners DEBUG 2024-09-03 07:04:21,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 155 finished +galaxy.jobs INFO 2024-09-03 07:04:21,315 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 156 in /galaxy/server/database/jobs_directory/000/156 +galaxy.model.metadata DEBUG 2024-09-03 07:04:21,333 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 180 +galaxy.jobs INFO 2024-09-03 07:04:21,365 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 155 in /galaxy/server/database/jobs_directory/000/155 +galaxy.jobs DEBUG 2024-09-03 07:04:21,383 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 156 executed (134.629 ms) +galaxy.jobs DEBUG 2024-09-03 07:04:21,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 155 executed (109.403 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:21,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 156 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:21,531 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking if job 155 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:04:21,871 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 157 +tpv.core.entities DEBUG 2024-09-03 07:04:21,903 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:04:21,904 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:04:21,909 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:04:21,922 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:04:21,939 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Working directory for job is: /galaxy/server/database/jobs_directory/000/157 +galaxy.jobs.runners DEBUG 2024-09-03 07:04:21,950 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [157] queued (40.708 ms) +galaxy.jobs.handler INFO 2024-09-03 07:04:21,952 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (157) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:21,955 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 157 +galaxy.jobs DEBUG 2024-09-03 07:04:22,011 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [157] prepared (46.348 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 07:04:22,011 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:04:22,011 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:04:22,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 07:04:22,234 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/157/tool_script.sh] for tool command [vcfcommonsamples '/galaxy/server/database/objects/1/0/4/dataset_104dbe11-503a-49b5-ab60-b2bcf328fdaf.dat' '/galaxy/server/database/objects/2/a/a/dataset_2aaee688-aad9-4401-b8f5-54a8cca3d4e0.dat' > '/galaxy/server/database/objects/7/e/2/dataset_7e2f22b7-bfbf-47ec-a19c-c188d884f442.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:04:22,253 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (157) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/157/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/157/galaxy_157.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:22,272 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 157 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 07:04:22,281 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:04:22,281 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:04:22,302 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:22,328 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 157 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:22,968 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:32,131 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-ptvnf with k8s id: gxy-ptvnf succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:04:32,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 157: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 07:04:39,392 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 157 finished +galaxy.model.metadata DEBUG 2024-09-03 07:04:39,434 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 182 +galaxy.jobs INFO 2024-09-03 07:04:39,461 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 157 in /galaxy/server/database/jobs_directory/000/157 +galaxy.jobs DEBUG 2024-09-03 07:04:39,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 157 executed (95.446 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:39,519 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 157 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:04:42,307 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 158 +tpv.core.entities DEBUG 2024-09-03 07:04:42,333 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:24.1.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:04:42,334 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:04:42,337 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:04:42,349 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:04:42,368 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Working directory for job is: /galaxy/server/database/jobs_directory/000/158 +galaxy.jobs.runners DEBUG 2024-09-03 07:04:42,376 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [158] queued (38.271 ms) +galaxy.jobs.handler INFO 2024-09-03 07:04:42,378 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (158) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:42,380 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 158 +galaxy.jobs DEBUG 2024-09-03 07:04:42,467 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [158] prepared (79.580 ms) +galaxy.jobs.command_factory INFO 2024-09-03 07:04:42,489 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/158/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/158/registry.xml' '/galaxy/server/database/jobs_directory/000/158/upload_params.json' '183:/galaxy/server/database/objects/c/d/9/dataset_cd94dda2-9ce9-4bae-8d7a-f3284c5d6167_files:/galaxy/server/database/objects/c/d/9/dataset_cd94dda2-9ce9-4bae-8d7a-f3284c5d6167.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:04:42,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (158) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/158/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/158/galaxy_158.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:42,510 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 158 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:42,525 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 158 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:43,158 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:52,287 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-zmpqr with k8s id: gxy-zmpqr succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:04:52,414 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 158: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 07:04:59,372 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 158 finished +galaxy.model.metadata DEBUG 2024-09-03 07:04:59,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 183 +galaxy.jobs INFO 2024-09-03 07:04:59,448 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 158 in /galaxy/server/database/jobs_directory/000/158 +galaxy.jobs DEBUG 2024-09-03 07:04:59,494 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 158 executed (101.381 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:59,508 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 158 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.handler DEBUG 2024-09-03 07:04:59,652 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 159 +tpv.core.entities DEBUG 2024-09-03 07:04:59,679 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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:24.1.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-03 07:04:59,679 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-03 07:04:59,683 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-03 07:04:59,694 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-03 07:04:59,706 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Working directory for job is: /galaxy/server/database/jobs_directory/000/159 +galaxy.jobs.runners DEBUG 2024-09-03 07:04:59,714 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [159] queued (30.375 ms) +galaxy.jobs.handler INFO 2024-09-03 07:04:59,716 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (159) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:59,719 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 159 +galaxy.jobs DEBUG 2024-09-03 07:04:59,767 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [159] prepared (40.562 ms) +galaxy.tool_util.deps.containers INFO 2024-09-03 07:04:59,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:04:59,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:04:59,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-03 07:04:59,811 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/159/tool_script.sh] for tool command [cat '/galaxy/server/database/objects/c/d/9/dataset_cd94dda2-9ce9-4bae-8d7a-f3284c5d6167.dat' | vcfdistance > '/galaxy/server/database/objects/f/a/a/dataset_faaf6962-d720-4a28-9440-955709a9f7cd.dat'] +galaxy.jobs.runners DEBUG 2024-09-03 07:04:59,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (159) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/159/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/159/galaxy_159.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:59,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 159 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.tool_util.deps.containers INFO 2024-09-03 07:04:59,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-03 07:04:59,834 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-09-03 07:04:59,856 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:04:59,872 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking if job 159 is an interactive tool. guest ports: []. interactive entry points: [] +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:05:00,314 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job set to running... +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:05:04,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.monitor_thread] Job id: gxy-75h2p with k8s id: gxy-75h2p succeeded +galaxy.jobs.runners DEBUG 2024-09-03 07:05:04,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 159: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-03 07:05:11,594 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 159 finished +galaxy.model.metadata DEBUG 2024-09-03 07:05:11,636 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 184 +galaxy.jobs INFO 2024-09-03 07:05:11,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 159 in /galaxy/server/database/jobs_directory/000/159 +galaxy.jobs DEBUG 2024-09-03 07:05:11,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 159 executed (94.410 ms) +galaxy.jobs.runners.kubernetes DEBUG 2024-09-03 07:05:11,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking if job 159 is an interactive tool. guest ports: []. interactive entry points: [] diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/jobs.txt b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/jobs.txt new file mode 100644 index 000000000..ea0987887 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/jobs.txt @@ -0,0 +1,159 @@ +4b02a6855a4b807b ok 2024-09-03T07:05:11.665993 toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/1.0.0_rc3+galaxy0 +a03238cf59f59304 ok 2024-09-03T07:04:59.450973 upload1 +00e9c169862726a9 ok 2024-09-03T07:04:39.464305 toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0 +07bd73e8fa8b74fa ok 2024-09-03T07:04:21.367701 upload1 +ce7e732c31d9ead0 ok 2024-09-03T07:04:21.318738 upload1 +b17c5c82cd3ecfce ok 2024-09-03T07:04:02.231885 upload1 +5cfa2c742a69011a ok 2024-09-03T07:04:01.060876 upload1 +ac7f57a7a56a19b0 error 2024-09-03T07:03:53.617492 upload1 +d486de5d89b20555 ok 2024-09-03T07:03:41.033029 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10 +35ff7e90998c8cd2 ok 2024-09-03T07:03:28.987962 upload1 +070fd72f262e6305 ok 2024-09-03T07:03:10.950493 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10 +c2ead3138e662556 ok 2024-09-03T07:02:52.713916 upload1 +3ecfb97d326c16cf ok 2024-09-03T07:02:32.601987 toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1 +cd15ced39043732a ok 2024-09-03T07:02:20.509904 upload1 +2841ee9a8ba77b56 ok 2024-09-03T07:02:02.198634 toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1 +97d5fce5154a6645 ok 2024-09-03T07:01:44.042295 upload1 +c56d003b54f034be ok 2024-09-03T07:01:24.817291 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +b1314eb67a4dcd5a ok 2024-09-03T07:01:11.928724 upload1 +b88fe9f6668d305b ok 2024-09-03T07:00:52.665417 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +e2c84b674ab0a58a ok 2024-09-03T07:00:39.579038 upload1 +4f537bd59150836b ok 2024-09-03T07:00:21.520023 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +0370dbf526dc9b2b ok 2024-09-03T07:00:08.404950 upload1 +98623284f686bc7c error 2024-09-03T06:59:49.873153 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +41280b56948002c0 ok 2024-09-03T06:59:44.763576 upload1 +db8ee8927138dbc6 error 2024-09-03T06:59:27.564655 upload1 +c70250f1936d4dbf ok 2024-09-03T06:59:16.518436 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +312b94f173dc392f ok 2024-09-03T06:59:03.333020 upload1 +16409116e0085a10 ok 2024-09-03T06:58:44.819387 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +2446f7b193ccd43f ok 2024-09-03T06:58:32.744730 upload1 +60dc8ed2ca8581ac error 2024-09-03T06:58:14.627333 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +156ba8706e2576b1 ok 2024-09-03T06:58:10.053693 upload1 +f9ab1f8db539c4c2 ok 2024-09-03T06:58:09.007910 upload1 +519c268d6e571334 ok 2024-09-03T06:57:50.152654 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +731c4dc86177d504 ok 2024-09-03T06:57:37.609571 upload1 +bed5eec7bbeb2165 ok 2024-09-03T06:57:37.533377 upload1 +5b57a0ab1389de76 ok 2024-09-03T06:57:17.681915 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +1b76baa431b0b231 ok 2024-09-03T06:57:05.467763 upload1 +67ce37012055eb04 ok 2024-09-03T06:56:47.495312 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +48da646b01255f7e ok 2024-09-03T06:56:34.504133 upload1 +cbcc5d5ae36a8e0d ok 2024-09-03T06:56:34.432698 upload1 +5af00f33c55c183a ok 2024-09-03T06:56:15.876307 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +cbf3c808415d120d ok 2024-09-03T06:55:57.848084 upload1 +d1834105c588e444 ok 2024-09-03T06:55:57.056866 upload1 +4a45112de13adf14 ok 2024-09-03T06:55:37.182150 toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0 +d3313b4961f32071 ok 2024-09-03T06:55:01.626221 toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2 +ddaa30e73593b3e5 ok 2024-09-03T06:54:18.112657 upload1 +3316eddaf4251de1 ok 2024-09-03T06:53:57.030427 toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2 +862aea799b88fbcb ok 2024-09-03T06:53:44.059426 upload1 +9289a2d1390a23f3 ok 2024-09-03T06:53:44.017143 upload1 +e5bbc2df36210b85 ok 2024-09-03T06:53:24.438425 toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2 +299b1d8b8909ae62 ok 2024-09-03T06:53:07.829743 upload1 +a605a831a031645f ok 2024-09-03T06:53:06.796666 upload1 +101b56dd69096d11 error 2024-09-03T06:52:46.150783 toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3 +f422d8c3699c8315 ok 2024-09-03T06:52:31.112502 upload1 +1b386e010a78b119 ok 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2024-09-03T06:49:59.062300 toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1 +080ffbad63804d16 ok 2024-09-03T06:49:43.456343 upload1 +2e8d1887c71f7a8c ok 2024-09-03T06:49:42.589618 upload1 +bfab2119ff8b913e ok 2024-09-03T06:49:42.474624 upload1 +07ddd8ef187d4c6f ok 2024-09-03T06:49:19.314762 toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1 +72ec8975d4ac13fa ok 2024-09-03T06:49:04.212406 upload1 +6c8cd3abced55ce4 ok 2024-09-03T06:48:44.804105 toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1 +eaf8e70c10dd6e28 ok 2024-09-03T06:48:09.655416 upload1 +25deebca7897c47d ok 2024-09-03T06:47:48.717504 toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1 +953735ae9d7cd0a9 ok 2024-09-03T06:47:15.267626 upload1 +689616360e4c010a ok 2024-09-03T06:47:15.175049 upload1 +f991bfa05ca6802d ok 2024-09-03T06:47:15.117660 upload1 +f4d9f721b3cdb075 ok 2024-09-03T06:46:49.299950 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +be283143aabb64cc ok 2024-09-03T06:46:37.400702 upload1 +95e5dec2fbf26496 error 2024-09-03T06:46:19.068042 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +6f9ddc11486f4483 ok 2024-09-03T06:46:13.997854 upload1 +b482f8a261be8211 ok 2024-09-03T06:45:55.948875 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +3fd5e57d74aeb532 ok 2024-09-03T06:45:43.846006 upload1 +3508b419fad98b48 ok 2024-09-03T06:45:25.617301 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +514792bee5a34ed2 ok 2024-09-03T06:45:13.555961 upload1 +151f5ee1dcce6a68 ok 2024-09-03T06:44:55.241716 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +a79070d45b9fb5f5 ok 2024-09-03T06:44:43.280903 upload1 +37d6ed51634e8761 ok 2024-09-03T06:44:24.022292 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +479bdc2f323f32d5 ok 2024-09-03T06:44:11.345191 upload1 +f4256d0ac94eef07 ok 2024-09-03T06:43:52.812734 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +e512b6f2b4539552 ok 2024-09-03T06:43:39.883634 upload1 +5ddc28fa07906217 ok 2024-09-03T06:43:21.806856 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +26d4fcf38cf42984 ok 2024-09-03T06:43:09.650873 upload1 +8465590ca68609af ok 2024-09-03T06:42:51.626405 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +17cf11e347d9df49 ok 2024-09-03T06:42:38.456501 upload1 +f5a56efeb8bb81a8 ok 2024-09-03T06:42:20.285014 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +cd27e3d7c5396c96 ok 2024-09-03T06:42:06.362977 upload1 +8c6501ef7470c2c5 ok 2024-09-03T06:41:48.023360 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +723204b635047d2d ok 2024-09-03T06:41:35.809947 upload1 +f22c1b2d1e045f2f ok 2024-09-03T06:41:17.668612 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +14126670676de88e ok 2024-09-03T06:41:04.647501 upload1 +4201e82de1a5b537 ok 2024-09-03T06:40:45.479656 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +298614057cf949c6 ok 2024-09-03T06:40:32.508099 upload1 +1fea3469de8b10eb ok 2024-09-03T06:40:14.189826 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +74c31b4c3f6ca54b ok 2024-09-03T06:40:01.249761 upload1 +17eba957cb30ed6d ok 2024-09-03T06:39:42.718953 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +1c4990bdd00112d8 ok 2024-09-03T06:39:30.878279 upload1 +7e4f207331dfd40e ok 2024-09-03T06:39:12.679583 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +b8489c15a5418aa1 ok 2024-09-03T06:38:59.641676 upload1 +8a480d7f0222dcfc ok 2024-09-03T06:38:42.429101 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +2c2b2362273f0801 ok 2024-09-03T06:38:29.257313 upload1 +f13374bcc7f5a6be ok 2024-09-03T06:38:10.182416 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +efcadb71aa692393 ok 2024-09-03T06:37:58.203864 upload1 +f6ad841bb200e556 ok 2024-09-03T06:37:39.953912 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +f5a3f30eee5746e9 ok 2024-09-03T06:37:26.911922 upload1 +ddf248f53d379e98 error 2024-09-03T06:37:07.586421 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +04be3fcc63c7ff40 ok 2024-09-03T06:37:02.489952 upload1 +14a8f68d665c01a1 ok 2024-09-03T06:36:44.085336 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +dd38e7891c4d4385 ok 2024-09-03T06:36:31.961898 upload1 +57520598933c3fed ok 2024-09-03T06:36:13.964630 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +849c4506f7ff365b ok 2024-09-03T06:36:01.875040 upload1 +5d83826b224ed5bd ok 2024-09-03T06:35:44.627152 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +e5e36224a481962e ok 2024-09-03T06:35:31.599266 upload1 +985a619d6854de88 ok 2024-09-03T06:35:12.634277 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +e68c72fe92db49a4 ok 2024-09-03T06:34:59.390053 upload1 +1e0ca3198f45ab6b ok 2024-09-03T06:34:41.233657 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +a988b3758b1cf6df ok 2024-09-03T06:34:28.123159 upload1 +e5e8cd249a50a76f ok 2024-09-03T06:34:08.995785 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +4116c1de5a40792c ok 2024-09-03T06:33:56.957378 upload1 +f92ede2d6e839cb1 error 2024-09-03T06:33:38.588827 upload1 +c18be95c05ac52c6 ok 2024-09-03T06:33:27.432694 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +10ea677b4495a336 ok 2024-09-03T06:33:14.405280 upload1 +c897c618250cf7d5 ok 2024-09-03T06:32:56.244021 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +cf4925c22d908ffb ok 2024-09-03T06:32:42.964083 upload1 +abad5501dcd12988 ok 2024-09-03T06:32:24.758224 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +46c327a6d434e72f ok 2024-09-03T06:32:11.809969 upload1 +7031160045e6798a ok 2024-09-03T06:31:53.579134 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +5289d5954fed9550 ok 2024-09-03T06:31:40.531729 upload1 +b00016d73b432039 error 2024-09-03T06:31:23.310575 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +e9f7c7443e767705 ok 2024-09-03T06:31:17.063719 upload1 +e568629811fc8172 error 2024-09-03T06:30:58.809528 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +02710b4481840932 ok 2024-09-03T06:30:45.530336 upload1 +cddc15d48be5f26e ok 2024-09-03T06:30:26.361078 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +a4f6ceefe39eba95 ok 2024-09-03T06:30:13.493089 upload1 +0598013d15530eee ok 2024-09-03T06:29:55.049063 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +06a7ae93479edc6f ok 2024-09-03T06:29:37.073629 upload1 +fe8ea7347ff1b547 ok 2024-09-03T06:29:17.851750 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0 +61497926af45aba7 ok 2024-09-03T06:29:04.561967 upload1 +23615efc68edca36 ok 2024-09-03T06:28:46.702767 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.3.2.0.0 +cd155ed83a2ec634 ok 2024-09-03T06:28:12.199282 upload1 +22f057fa51fff74b ok 2024-09-03T06:27:53.001050 toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0 +03b1d146c8da1044 ok 2024-09-03T06:27:41.488357 upload1 +dc997c570f96510e ok 2024-09-03T06:27:40.396490 upload1 +b8ae0f015a2e06aa ok 2024-09-03T06:27:20.692623 toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0 +a80664568881873a ok 2024-09-03T06:26:42.921847 upload1 +c5fe43971bba42f1 ok 2024-09-03T06:26:42.797940 upload1 diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/node-info.txt b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/node-info.txt new file mode 100644 index 000000000..026e032ba --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/node-info.txt @@ -0,0 +1,147 @@ +Name: gke-edge-24-09-03-06-11-default-pool-983e958e-vtp1 +Roles: +Labels: beta.kubernetes.io/arch=amd64 + beta.kubernetes.io/instance-type=e2-custom-20-81920 + beta.kubernetes.io/os=linux + cloud.google.com/gke-boot-disk=pd-balanced + cloud.google.com/gke-container-runtime=containerd + cloud.google.com/gke-cpu-scaling-level=20 + cloud.google.com/gke-logging-variant=DEFAULT + cloud.google.com/gke-max-pods-per-node=110 + cloud.google.com/gke-memory-gb-scaling-level=81 + cloud.google.com/gke-nodepool=default-pool + cloud.google.com/gke-os-distribution=cos + cloud.google.com/gke-provisioning=standard + cloud.google.com/gke-stack-type=IPV4 + cloud.google.com/machine-family=e2 + cloud.google.com/private-node=false + failure-domain.beta.kubernetes.io/region=us-east1 + failure-domain.beta.kubernetes.io/zone=us-east1-b + kubernetes.io/arch=amd64 + kubernetes.io/hostname=gke-edge-24-09-03-06-11-default-pool-983e958e-vtp1 + 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: 4796281349377562606 + csi.volume.kubernetes.io/nodeid: + {"cvmfs.csi.cern.ch":"gke-edge-24-09-03-06-11-default-pool-983e958e-vtp1","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: Tue, 03 Sep 2024 06:17:52 +0000 +Taints: +Unschedulable: false +Lease: + HolderIdentity: gke-edge-24-09-03-06-11-default-pool-983e958e-vtp1 + AcquireTime: + RenewTime: Tue, 03 Sep 2024 07:05:38 +0000 +Conditions: + Type Status LastHeartbeatTime LastTransitionTime Reason Message + ---- ------ ----------------- ------------------ ------ ------- + ReadonlyFilesystem False Tue, 03 Sep 2024 07:02:57 +0000 Tue, 03 Sep 2024 06:17:52 +0000 FilesystemIsNotReadOnly Filesystem is not read-only + DeprecatedMirrorsFieldInContainerdConfiguration False Tue, 03 Sep 2024 07:02:57 +0000 Tue, 03 Sep 2024 06:17:52 +0000 DeprecatedMirrorsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'mirrors' field in containerd's config + FrequentDockerRestart False Tue, 03 Sep 2024 07:02:57 +0000 Tue, 03 Sep 2024 06:17:52 +0000 NoFrequentDockerRestart docker is functioning properly + DeprecatedConfigsFieldInContainerdConfiguration False Tue, 03 Sep 2024 07:02:57 +0000 Tue, 03 Sep 2024 06:17:52 +0000 DeprecatedConfigsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'configs' field in containerd's config + DeprecatedOtherContainerdFeatures False Tue, 03 Sep 2024 07:02:57 +0000 Tue, 03 Sep 2024 06:17:52 +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. + DeprecatedPullingSchemaV1Image False Tue, 03 Sep 2024 07:02:57 +0000 Tue, 03 Sep 2024 06:17:52 +0000 DeprecatedPullingSchemaV1ImageDetected No deprecation risk: did not pull any schema v1 images + DeprecatedAuthsFieldInContainerdConfiguration False Tue, 03 Sep 2024 07:02:57 +0000 Tue, 03 Sep 2024 06:17:52 +0000 DeprecatedAuthsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'auths' field in containerd's config + DeprecatedUsingV1Alpha2Cri False Tue, 03 Sep 2024 07:02:57 +0000 Tue, 03 Sep 2024 06:17:52 +0000 DeprecatedUsingV1Alpha2CriNotDetected No deprecation risk: did not use v1alpha2 CRI + CorruptDockerOverlay2 False Tue, 03 Sep 2024 07:02:57 +0000 Tue, 03 Sep 2024 06:17:52 +0000 NoCorruptDockerOverlay2 docker overlay2 is functioning properly + KernelDeadlock False Tue, 03 Sep 2024 07:02:57 +0000 Tue, 03 Sep 2024 06:17:52 +0000 KernelHasNoDeadlock kernel has no deadlock + FrequentKubeletRestart False Tue, 03 Sep 2024 07:02:57 +0000 Tue, 03 Sep 2024 06:17:52 +0000 NoFrequentKubeletRestart kubelet is functioning properly + FrequentContainerdRestart False Tue, 03 Sep 2024 07:02:57 +0000 Tue, 03 Sep 2024 06:17:52 +0000 NoFrequentContainerdRestart containerd is functioning properly + FrequentUnregisterNetDevice False Tue, 03 Sep 2024 07:02:57 +0000 Tue, 03 Sep 2024 06:17:52 +0000 NoFrequentUnregisterNetDevice node is functioning properly + SysctlChanged False Tue, 03 Sep 2024 07:02:57 +0000 Tue, 03 Sep 2024 06:17:52 +0000 SysctlNotChanged Default sysctls are in effect, no unexpected sysctl changes + NetworkUnavailable False Tue, 03 Sep 2024 06:17:53 +0000 Tue, 03 Sep 2024 06:17:53 +0000 RouteCreated NodeController create implicit route + MemoryPressure False Tue, 03 Sep 2024 07:04:51 +0000 Tue, 03 Sep 2024 06:17:24 +0000 KubeletHasSufficientMemory kubelet has sufficient memory available + DiskPressure False Tue, 03 Sep 2024 07:04:51 +0000 Tue, 03 Sep 2024 06:17:24 +0000 KubeletHasNoDiskPressure kubelet has no disk pressure + PIDPressure False Tue, 03 Sep 2024 07:04:51 +0000 Tue, 03 Sep 2024 06:17:24 +0000 KubeletHasSufficientPID kubelet has sufficient PID available + Ready True Tue, 03 Sep 2024 07:04:51 +0000 Tue, 03 Sep 2024 06:18:12 +0000 KubeletReady kubelet is posting ready status +Addresses: + InternalIP: 10.142.15.223 + ExternalIP: 34.23.21.190 +Capacity: + cpu: 20 + ephemeral-storage: 98831908Ki + hugepages-1Gi: 0 + hugepages-2Mi: 0 + memory: 82368036Ki + pods: 110 +Allocatable: + cpu: 19880m + ephemeral-storage: 47060071478 + hugepages-1Gi: 0 + hugepages-2Mi: 0 + memory: 75553316Ki + pods: 110 +System Info: + Machine ID: 4a42875b3a61a6a3614afcf907952ee6 + System UUID: 4a42875b-3a61-a6a3-614a-fcf907952ee6 + Boot ID: 27b2fae7-8be5-4367-9826-305a3ce8ad9e + Kernel Version: 6.1.90+ + OS Image: Container-Optimized OS from Google + Operating System: linux + Architecture: amd64 + Container Runtime Version: containerd://1.7.15 + Kubelet Version: v1.30.2-gke.1587003 + Kube-Proxy Version: v1.30.2-gke.1587003 +PodCIDR: 10.16.0.0/24 +PodCIDRs: 10.16.0.0/24 +ProviderID: gce://anvil-and-terra-development/us-east1-b/gke-edge-24-09-03-06-11-default-pool-983e958e-vtp1 +Non-terminated Pods: (27 in total) + Namespace Name CPU Requests CPU Limits Memory Requests Memory Limits Age + --------- ---- ------------ ---------- --------------- ------------- --- + edge-24-09-03-06-11-1 edge-24-09-03-06-11-1-cvmfscsi-controllerplugin-6fdfccf5597dvrb 0 (0%) 0 (0%) 0 (0%) 0 (0%) 45m + edge-24-09-03-06-11-1 edge-24-09-03-06-11-1-cvmfscsi-nodeplugin-kdnsn 0 (0%) 0 (0%) 0 (0%) 0 (0%) 41m + edge-24-09-03-06-11-1 edge-24-09-03-06-11-1-galaxy-celery-66656fc576-q7dq2 500m (2%) 2 (10%) 2G (2%) 8G (10%) 45m + edge-24-09-03-06-11-1 edge-24-09-03-06-11-1-galaxy-celery-beat-75d576dbfc-68cxc 500m (2%) 2 (10%) 2G (2%) 8G (10%) 45m + edge-24-09-03-06-11-1 edge-24-09-03-06-11-1-galaxy-galaxy-postgres-0 250m (1%) 0 (0%) 256Mi (0%) 0 (0%) 45m + edge-24-09-03-06-11-1 edge-24-09-03-06-11-1-galaxy-job-0-54c68c5bbf-z9wrv 500m (2%) 2 (10%) 2G (2%) 8G (10%) 45m + edge-24-09-03-06-11-1 edge-24-09-03-06-11-1-galaxy-nginx-6cbcb5977-v98mz 100m (0%) 2 (10%) 500M (0%) 3G (3%) 45m + edge-24-09-03-06-11-1 edge-24-09-03-06-11-1-galaxy-rabbitmq-server-server-0 1 (5%) 2 (10%) 2Gi (2%) 2Gi (2%) 45m + edge-24-09-03-06-11-1 edge-24-09-03-06-11-1-galaxy-web-5d96646bc-xt5hp 500m (2%) 2 (10%) 2G (2%) 8G (10%) 45m + edge-24-09-03-06-11-1 edge-24-09-03-06-11-1-galaxy-workflow-796c67d755-pmhp8 500m (2%) 2 (10%) 2G (2%) 8G (10%) 45m + edge-24-09-03-06-11-1 edge-24-09-03-06-11-1-nfs-0 0 (0%) 0 (0%) 0 (0%) 0 (0%) 45m + edge-24-09-03-06-11-1 edge-24-09-03-06-11-1-rabbitmq-64f5b5c798-b79rg 0 (0%) 0 (0%) 0 (0%) 0 (0%) 45m + edge-24-09-03-06-11-1 edge-24-09-03-06-11-1-rabbitmq-messaging-topology-operator9v9qs 0 (0%) 0 (0%) 0 (0%) 0 (0%) 45m + gke-managed-cim kube-state-metrics-0 105m (0%) 0 (0%) 130Mi (0%) 530Mi (0%) 48m + gmp-system collector-mztgr 5m (0%) 0 (0%) 36M (0%) 3032M (3%) 47m + gmp-system gmp-operator-7fbf499987-gd457 1m (0%) 0 (0%) 16M (0%) 2G (2%) 48m + kube-system event-exporter-gke-64f56d6fd9-bfp4k 3m (0%) 0 (0%) 100Mi (0%) 0 (0%) 48m + kube-system fluentbit-gke-kdb9p 105m (0%) 1 (5%) 230Mi (0%) 530Mi (0%) 47m + kube-system gke-metrics-agent-x9566 19m (0%) 1 (5%) 155Mi (0%) 155Mi (0%) 47m + kube-system konnectivity-agent-78ddf5898f-rr2tv 15m (0%) 0 (0%) 60Mi (0%) 155Mi (0%) 48m + kube-system konnectivity-agent-autoscaler-6796d65955-h6dnz 10m (0%) 0 (0%) 10M (0%) 0 (0%) 48m + kube-system kube-dns-745cf4c555-f8lnz 265m (1%) 0 (0%) 140Mi (0%) 240Mi (0%) 49m + kube-system kube-dns-autoscaler-5fc4c6f47f-96fqj 20m (0%) 0 (0%) 10Mi (0%) 0 (0%) 49m + kube-system kube-proxy-gke-edge-24-09-03-06-11-default-pool-983e958e-vtp1 100m (0%) 0 (0%) 0 (0%) 0 (0%) 47m + kube-system l7-default-backend-66b5dbbfbd-zw7df 10m (0%) 0 (0%) 20Mi (0%) 0 (0%) 48m + kube-system metrics-server-v0.7.1-7b797b78c7-b2nfr 48m (0%) 43m (0%) 105Mi (0%) 355Mi (0%) 47m + kube-system pdcsi-node-bh7fg 10m (0%) 0 (0%) 20Mi (0%) 100Mi (0%) 47m +Allocated resources: + (Total limits may be over 100 percent, i.e., overcommitted.) + Resource Requests Limits + -------- -------- ------ + cpu 4566m (22%) 16043m (80%) + memory 13995037824 (18%) 52344793088 (67%) + 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 47m kube-proxy + Normal Starting 52m kubelet Starting kubelet. + Warning InvalidDiskCapacity 52m kubelet invalid capacity 0 on image filesystem + Normal NodeAllocatableEnforced 52m kubelet Updated Node Allocatable limit across pods + Normal NodeHasNoDiskPressure 50m (x7 over 52m) kubelet Node gke-edge-24-09-03-06-11-default-pool-983e958e-vtp1 status is now: NodeHasNoDiskPressure + Normal NodeHasSufficientPID 50m (x7 over 52m) kubelet Node gke-edge-24-09-03-06-11-default-pool-983e958e-vtp1 status is now: NodeHasSufficientPID + Normal NodeHasSufficientMemory 49m (x8 over 52m) kubelet Node gke-edge-24-09-03-06-11-default-pool-983e958e-vtp1 status is now: NodeHasSufficientMemory + Warning NodeRegistrationCheckerStart 47m node-registration-checker-monitor Tue Sep 3 06:13:45 UTC 2024 - ** Starting Node Registration Checker ** + Normal Synced 47m cloud-node-controller Node synced successfully + Normal RegisteredNode 47m node-controller Node gke-edge-24-09-03-06-11-default-pool-983e958e-vtp1 event: Registered Node gke-edge-24-09-03-06-11-default-pool-983e958e-vtp1 in Controller + Warning NodeRegistrationCheckerDidNotRunChecks 45m node-registration-checker-monitor Tue Sep 3 06:20:46 UTC 2024 - ** Node ready and registered. ** diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/results.html b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/results.html new file mode 100644 index 000000000..2c1621fe4 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/results.html @@ -0,0 +1,291 @@ + + + + + + + Test Results (powered by Planemo) + + + + + + + + + + +
+
+
+
+ + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/results.json b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/results.json new file mode 100644 index 000000000..9f1ed803e --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 72, "errors": 4, "failures": 7, "skips": 1}, "tests": [{"id": "bcftools_csq/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_csq", "tool_version": "1.10", "test_index": 0, "time_seconds": 20.08892250061035, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_csq/1.10-1", "has_data": true, "data": {"tool_id": "bcftools_csq", "tool_version": "1.10", "test_index": 1, "status": "skip"}}, {"id": "bcftools_plugin_mendelian/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_plugin_mendelian", "tool_version": "1.10", "test_index": 0, "time_seconds": 36.71414375305176, "inputs": {"input_file": {"src": "hda", "id": "cd3a9e0b60df09f3"}, "sec_plugin|trios|mother": "NA00001", "sec_plugin|trios|father": "NA00002", "sec_plugin|trios|child": "NA00006", "sec_plugin|trios|trios_src": "trio", "sec_plugin|mode": "delete", "output_type": "v"}, "job": {"model_class": "Job", "id": "070fd72f262e6305", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T07:02:53.015377", "update_time": "2024-09-03T07:03:10.950493", "galaxy_version": "24.1", "external_id": "gxy-zll6z", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/0/a/7/dataset_0a73327e-d103-4fbf-bfe1-65608e386907.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin mendelian --output-type 'v' input.vcf.gz --trio \"NA00001,NA00002,NA00006\" --delete 2> tmp_stderr > '/galaxy/server/database/objects/c/c/a/dataset_ccac2b28-fe1a-4e8e-bd2a-2ab1d64054ba.dat' && cat tmp_stderr", "user_email": "tests@fake.org", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_plugin": "{\"mode\": \"delete\", \"trios\": {\"__current_case__\": 0, \"child\": \"NA00006\", \"father\": \"NA00002\", \"mother\": \"NA00001\", \"trios_src\": \"trio\"}}", "sec_restrict": "{\"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}"}, "inputs": {"input_file": {"id": "cd3a9e0b60df09f3", "src": "hda", "uuid": "0a73327e-d103-4fbf-bfe1-65608e386907"}}, "outputs": {"output_file": {"id": "8dbd713a3c5d94a5", "src": "hda", "uuid": "ccac2b28-fe1a-4e8e-bd2a-2ab1d64054ba"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "# [1]nOK\t[2]nBad\t[3]nSkipped\t[4]Trio (mother,father,child)\n20\t13\t0\tNA00001,NA00002,NA00006\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "# [1]nOK\t[2]nBad\t[3]nSkipped\t[4]Trio (mother,father,child)\n20\t13\t0\tNA00001,NA00002,NA00006\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-03 07:02:59", "plugin": "core", "name": "end_epoch", "raw_value": "1725346979.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 07:02:58", "plugin": "core", "name": "start_epoch", "raw_value": "1725346978.0000000"}, {"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_plugin_mendelian/1.10-1", "has_data": true, "data": {"tool_id": "bcftools_plugin_mendelian", "tool_version": "1.10", "test_index": 1, "time_seconds": 29.868834018707275, "inputs": {"input_file": {"src": "hda", "id": "3e91297e238bfe22"}, "sec_plugin|trios|mother": "NA00001", "sec_plugin|trios|father": "NA00002", "sec_plugin|trios|child": "NA00006", "sec_plugin|trios|trios_src": "trio", "sec_plugin|mode": "x", "output_type": "v"}, "job": {"model_class": "Job", "id": "d486de5d89b20555", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_mendelian/bcftools_plugin_mendelian/1.10", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T07:03:29.347000", "update_time": "2024-09-03T07:03:41.033029", "galaxy_version": "24.1", "external_id": "gxy-pgnd2", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/2/6/dataset_f260f8ca-456c-4206-a345-aa84958fbc31.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin mendelian --output-type 'v' input.vcf.gz --trio \"NA00001,NA00002,NA00006\" --list x 2> tmp_stderr > '/galaxy/server/database/objects/5/5/b/dataset_55b77024-4ea0-4deb-b6b4-fafede920fb6.dat' && cat tmp_stderr", "user_email": "tests@fake.org", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_plugin": "{\"mode\": \"x\", \"trios\": {\"__current_case__\": 0, \"child\": \"NA00006\", \"father\": \"NA00002\", \"mother\": \"NA00001\", \"trios_src\": \"trio\"}}", "sec_restrict": "{\"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}"}, "inputs": {"input_file": {"id": "3e91297e238bfe22", "src": "hda", "uuid": "f260f8ca-456c-4206-a345-aa84958fbc31"}}, "outputs": {"output_file": {"id": "7dcd83d175dbd593", "src": "hda", "uuid": "55b77024-4ea0-4deb-b6b4-fafede920fb6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "# [1]nOK\t[2]nBad\t[3]nSkipped\t[4]Trio (mother,father,child)\n20\t13\t0\tNA00001,NA00002,NA00006\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "# [1]nOK\t[2]nBad\t[3]nSkipped\t[4]Trio (mother,father,child)\n20\t13\t0\tNA00001,NA00002,NA00006\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-03 07:03:31", "plugin": "core", "name": "end_epoch", "raw_value": "1725347011.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 07:03:30", "plugin": "core", "name": "start_epoch", "raw_value": "1725347010.0000000"}, {"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/0.0.1-0", "has_data": true, "data": {"tool_id": "column_remove_by_header", "tool_version": "0.0.1", "test_index": 0, "time_seconds": 36.695852279663086, "inputs": {"input_tabular": {"src": "hda", "id": "01d5902ce42d8c6d"}, "headers_0|name": "a", "keep_columns": false, "strip_characters": "#"}, "job": {"model_class": "Job", "id": "2841ee9a8ba77b56", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T07:01:44.246217", "update_time": "2024-09-03T07:02:02.198634", "galaxy_version": "24.1", "external_id": "gxy-pgtzf", "handler": null, "job_runner_name": null, "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/372967836e98/column_remove_by_header/column_remove_by_header.py' '/galaxy/server/database/objects/2/d/8/dataset_2d8defe6-9a1c-41a8-829c-4c9de99a08cc.dat' '/galaxy/server/database/objects/d/3/b/dataset_d3bda304-115e-4a00-a497-1d448cdbbdb7.dat' '\t' '' '#' 'a'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "strip_characters": "\"#\"", "keep_columns": "false", "headers": "[{\"__index__\": 0, \"name\": \"a\"}]"}, "inputs": {"input_tabular": {"id": "01d5902ce42d8c6d", "src": "hda", "uuid": "2d8defe6-9a1c-41a8-829c-4c9de99a08cc"}}, "outputs": {"output_tabular": {"id": "93c81e3a39e9634c", "src": "hda", "uuid": "d3bda304-115e-4a00-a497-1d448cdbbdb7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Kept 3 of 4 columns.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Kept 3 of 4 columns.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 07:01:51", "plugin": "core", "name": "end_epoch", "raw_value": "1725346911.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 07:01:51", "plugin": "core", "name": "start_epoch", "raw_value": "1725346911.0000000"}, {"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/0.0.1-1", "has_data": true, "data": {"tool_id": "column_remove_by_header", "tool_version": "0.0.1", "test_index": 1, "time_seconds": 30.126420497894287, "inputs": {"input_tabular": {"src": "hda", "id": "ac724ec88ec1dc52"}, "headers_0|name": "KEY", "headers_1|name": "a", "keep_columns": true, "strip_characters": "#"}, "job": {"model_class": "Job", "id": "3ecfb97d326c16cf", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T07:02:20.837781", "update_time": "2024-09-03T07:02:32.601987", "galaxy_version": "24.1", "external_id": "gxy-9dwlv", "handler": null, "job_runner_name": null, "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/372967836e98/column_remove_by_header/column_remove_by_header.py' '/galaxy/server/database/objects/9/0/5/dataset_90557dec-22a2-4d49-a45c-b902d28ba311.dat' '/galaxy/server/database/objects/b/9/2/dataset_b923e770-5fe7-4f3c-a82a-2e585fb02633.dat' '\t' '--keep' '#' 'KEY' 'a'", "user_email": "tests@fake.org", "command_version": "", "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": "ac724ec88ec1dc52", "src": "hda", "uuid": "90557dec-22a2-4d49-a45c-b902d28ba311"}}, "outputs": {"output_tabular": {"id": "99729eea27225c1d", "src": "hda", "uuid": "b923e770-5fe7-4f3c-a82a-2e585fb02633"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Kept 2 of 4 columns.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Kept 2 of 4 columns.\n", "stderr": "", "job_messages": [], 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"job_stderr": "", "stdout": "Groomed 2 sanger reads into illumina reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:36:03", "plugin": "core", "name": "end_epoch", "raw_value": "1725345363.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:36:03", "plugin": "core", "name": "start_epoch", "raw_value": "1725345363.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": 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"status": "success"}}, {"id": "fastq_groomer/1.1.5-17", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 17, "time_seconds": 30.310776233673096, "inputs": {"input_file": {"src": "hda", "id": "efcadb71aa692393"}, "input_type": "solexa", "options_type|output_type": "illumina", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "f13374bcc7f5a6be", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:37:58.300936", "update_time": "2024-09-03T06:38:10.182416", "galaxy_version": "24.1", "external_id": "gxy-rhl5n", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/a/7/8/dataset_a78c7ece-c8b8-4d27-99a7-0f935cee9df7.dat' solexa '/galaxy/server/database/objects/0/8/c/dataset_08c6d21e-1059-414e-8bbf-2ccafebf50fc.dat' illumina None summarize_input --fix-id", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"illumina\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"solexa\""}, "inputs": {"input_file": {"id": "efcadb71aa692393", "src": "hda", "uuid": "a78c7ece-c8b8-4d27-99a7-0f935cee9df7"}}, "outputs": {"output_file": {"id": "f13374bcc7f5a6be", "src": "hda", "uuid": "08c6d21e-1059-414e-8bbf-2ccafebf50fc"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Groomed 2 solexa reads into illumina reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Groomed 2 solexa reads into illumina reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:37:59", "plugin": "core", "name": "end_epoch", "raw_value": "1725345479.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:37:59", "plugin": "core", "name": "start_epoch", "raw_value": "1725345479.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-18", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 18, "time_seconds": 32.105528116226196, "inputs": {"input_file": {"src": "hda", "id": "2c2b2362273f0801"}, "input_type": "solexa", "options_type|output_type": "sanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "8a480d7f0222dcfc", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:38:29.528409", "update_time": "2024-09-03T06:38:42.429101", "galaxy_version": "24.1", "external_id": "gxy-n6gm2", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/e/f/3/dataset_ef35730b-2950-4b83-addf-d621ff7af483.dat' solexa '/galaxy/server/database/objects/a/7/6/dataset_a76078c0-ecce-4f57-acac-06c3969dc587.dat' sanger None summarize_input --fix-id", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"solexa\""}, "inputs": {"input_file": {"id": "2c2b2362273f0801", "src": "hda", "uuid": "ef35730b-2950-4b83-addf-d621ff7af483"}}, "outputs": {"output_file": {"id": "8a480d7f0222dcfc", "src": "hda", "uuid": "a76078c0-ecce-4f57-acac-06c3969dc587"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Groomed 2 solexa reads into sanger reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Groomed 2 solexa reads into sanger reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:38:31", "plugin": "core", "name": "end_epoch", "raw_value": "1725345511.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:38:31", "plugin": "core", "name": "start_epoch", "raw_value": "1725345511.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-19", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 19, "time_seconds": 30.28959631919861, "inputs": {"input_file": {"src": "hda", "id": "b8489c15a5418aa1"}, "input_type": "solexa", "options_type|output_type": "cssanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "7e4f207331dfd40e", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:38:59.855426", "update_time": "2024-09-03T06:39:12.679583", "galaxy_version": "24.1", "external_id": "gxy-xcm4m", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/7/e/1/dataset_7e1e85a9-9ed2-46f2-8b89-3f776375cd29.dat' solexa '/galaxy/server/database/objects/7/f/8/dataset_7f8e6fb2-8c43-41d1-8f3f-9579f05309f1.dat' cssanger None summarize_input --fix-id", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"cssanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"solexa\""}, "inputs": {"input_file": {"id": "b8489c15a5418aa1", "src": "hda", "uuid": "7e1e85a9-9ed2-46f2-8b89-3f776375cd29"}}, "outputs": {"output_file": {"id": "7e4f207331dfd40e", "src": "hda", "uuid": "7f8e6fb2-8c43-41d1-8f3f-9579f05309f1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Groomed 2 solexa reads into cssanger reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Groomed 2 solexa reads into cssanger reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:39:01", "plugin": "core", "name": "end_epoch", "raw_value": "1725345541.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:39:01", "plugin": "core", "name": "start_epoch", "raw_value": "1725345541.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-2", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 2, "time_seconds": 32.23112940788269, "inputs": {"input_file": {"src": "hda", "id": "02710b4481840932"}, "input_type": "sanger", "options_type|fix_id": false, "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "e568629811fc8172", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "state": "error", "exit_code": 1, "create_time": "2024-09-03T06:30:45.681757", "update_time": "2024-09-03T06:30:58.809528", "galaxy_version": "24.1", "external_id": "gxy-wqm8m", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/3/4/4/dataset_3443d596-7865-4b06-a918-b42375674ca6.dat' sanger '/galaxy/server/database/objects/f/d/3/dataset_fd35fc07-8dea-4bb5-b485-7bf007537abc.dat' sanger ascii summarize_input --no-fix-id", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": false, \"force_quality_encoding\": \"ascii\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"sanger\""}, "inputs": {"input_file": {"id": "02710b4481840932", "src": "hda", "uuid": "3443d596-7865-4b06-a918-b42375674ca6"}}, "outputs": {"output_file": {"id": "e568629811fc8172", "src": "hda", "uuid": "fd35fc07-8dea-4bb5-b485-7bf007537abc"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "There was an error reading your input file. Your input file is likely malformed.\nIt is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below.\nHowever, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism.\n\nThe reported error is: 'Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).'.\nThe error occurred at the start of your file and no valid FASTQ reads were found.\nThe error in your file occurs between lines '1' and '3', which corresponds to byte-offsets '0' and '33', and contains the text (33 of 33 bytes shown):\n\n@FAKE-1\nACGTACGTAC\n+invalid line\n\n", "tool_stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/gx-fastq-groomer\", line 10, in \n sys.exit(main())\n ^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 99, in main\n Groomer().run()\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 48, in run\n for read_count, fastq_read in enumerate(reader):\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 683, in __iter__\n yield next(self)\n ^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 742, in __next__\n raise e\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 724, in __next__\n block = super(fastqVerboseErrorReader, self).__next__()\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 621, in __next__\n self._read_fastq_sequence(rval, id_line)\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 666, in _read_fastq_sequence\n raise fastqFormatError(\ngalaxy_utils.sequence.fastq.fastqFormatError: Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).\n", "job_stdout": "", "job_stderr": "", "stdout": "There was an error reading your input file. Your input file is likely malformed.\nIt is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below.\nHowever, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism.\n\nThe reported error is: 'Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).'.\nThe error occurred at the start of your file and no valid FASTQ reads were found.\nThe error in your file occurs between lines '1' and '3', which corresponds to byte-offsets '0' and '33', and contains the text (33 of 33 bytes shown):\n\n@FAKE-1\nACGTACGTAC\n+invalid line\n\n", "stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/gx-fastq-groomer\", line 10, in \n sys.exit(main())\n ^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 99, in main\n Groomer().run()\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 48, in run\n for read_count, fastq_read in enumerate(reader):\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 683, in __iter__\n yield next(self)\n ^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 742, in __next__\n raise e\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 724, in __next__\n block = super(fastqVerboseErrorReader, self).__next__()\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 621, in __next__\n self._read_fastq_sequence(rval, id_line)\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 666, in _read_fastq_sequence\n raise fastqFormatError(\ngalaxy_utils.sequence.fastq.fastqFormatError: Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:30:47", "plugin": "core", "name": "start_epoch", "raw_value": "1725345047.0000000"}, {"title": "Job End Time", "value": "2024-09-03 06:30:48", "plugin": "core", "name": "end_epoch", "raw_value": "1725345048.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-20", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 20, "time_seconds": 29.899918794631958, "inputs": {"input_file": {"src": "hda", "id": "1c4990bdd00112d8"}, "input_type": "cssanger", "options_type|output_type": "cssanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "17eba957cb30ed6d", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:39:31.094875", "update_time": "2024-09-03T06:39:42.718953", "galaxy_version": "24.1", "external_id": "gxy-4s55p", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/a/0/9/dataset_a094c793-d2ba-4dd4-a923-37aa5b938c31.dat' cssanger '/galaxy/server/database/objects/2/4/1/dataset_2411f8ca-8095-4ca6-b237-15b7f45b5933.dat' cssanger None summarize_input --fix-id", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"cssanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "1c4990bdd00112d8", "src": "hda", "uuid": "a094c793-d2ba-4dd4-a923-37aa5b938c31"}}, "outputs": {"output_file": {"id": "17eba957cb30ed6d", "src": "hda", "uuid": "2411f8ca-8095-4ca6-b237-15b7f45b5933"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:39:32", "plugin": "core", "name": "end_epoch", "raw_value": "1725345572.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:39:32", "plugin": "core", "name": "start_epoch", "raw_value": "1725345572.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-21", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 21, "time_seconds": 31.563524961471558, "inputs": {"input_file": {"src": "hda", "id": "74c31b4c3f6ca54b"}, "input_type": "cssanger", "options_type|output_type": "sanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "1fea3469de8b10eb", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:40:01.396607", "update_time": "2024-09-03T06:40:14.189826", "galaxy_version": "24.1", "external_id": "gxy-lmncn", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/0/c/8/dataset_0c822b25-84a1-43b6-b86c-353817fe5f1f.dat' cssanger '/galaxy/server/database/objects/2/0/4/dataset_20464c28-d355-4e86-808f-5637246b7ea3.dat' sanger None summarize_input --fix-id", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "74c31b4c3f6ca54b", "src": "hda", "uuid": "0c822b25-84a1-43b6-b86c-353817fe5f1f"}}, "outputs": {"output_file": {"id": "1fea3469de8b10eb", "src": "hda", "uuid": "20464c28-d355-4e86-808f-5637246b7ea3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Groomed 2 cssanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:40:03", "plugin": "core", "name": "end_epoch", "raw_value": "1725345603.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:40:03", "plugin": "core", "name": "start_epoch", "raw_value": "1725345603.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-22", "has_data": true, 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cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Groomed 2 cssanger reads into illumina reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:40:34", "plugin": "core", "name": "end_epoch", "raw_value": "1725345634.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:40:34", "plugin": "core", "name": "start_epoch", "raw_value": "1725345634.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": 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'/galaxy/server/database/objects/f/c/3/dataset_fc368bde-3f7a-4f2c-9693-63c96fe7d3e3.dat' cssanger '/galaxy/server/database/objects/e/4/2/dataset_e42f9f92-4d00-403c-86d7-ff4079519f41.dat' solexa None summarize_input --fix-id", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"solexa\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "14126670676de88e", "src": "hda", "uuid": "fc368bde-3f7a-4f2c-9693-63c96fe7d3e3"}}, "outputs": {"output_file": {"id": "f22c1b2d1e045f2f", "src": "hda", "uuid": "e42f9f92-4d00-403c-86d7-ff4079519f41"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into solexa reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Groomed 2 cssanger reads into solexa reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:41:06", "plugin": "core", "name": "end_epoch", "raw_value": "1725345666.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:41:06", "plugin": "core", "name": "start_epoch", "raw_value": 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"", "stdout": "Groomed 2 cssanger.bz2 reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:46:39", "plugin": "core", "name": "end_epoch", "raw_value": "1725345999.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:46:39", "plugin": "core", "name": "start_epoch", "raw_value": "1725345999.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-4", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 4, "time_seconds": 30.53116011619568, "inputs": {"input_file": {"src": "hda", "id": "5289d5954fed9550"}, "input_type": "cssanger", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "7031160045e6798a", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:31:40.862786", "update_time": "2024-09-03T06:31:53.579134", "galaxy_version": "24.1", "external_id": "gxy-vsn67", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/2/a/e/dataset_2ae28f22-d864-4303-9934-3b3cf77d7af1.dat' cssanger '/galaxy/server/database/objects/3/d/d/dataset_3dd0903b-f73a-478d-bcee-94ec7b9a6004.dat' cssanger ascii summarize_input", "user_email": "tests@fake.org", "command_version": "", "params": {"input_type": "\"cssanger\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "5289d5954fed9550", "src": "hda", "uuid": "2ae28f22-d864-4303-9934-3b3cf77d7af1"}}, "outputs": {"output_file": {"id": "7031160045e6798a", "src": "hda", "uuid": "3dd0903b-f73a-478d-bcee-94ec7b9a6004"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:31:42", "plugin": "core", "name": "start_epoch", "raw_value": "1725345102.0000000"}, {"title": "Job End Time", "value": "2024-09-03 06:31:42", "plugin": "core", "name": "end_epoch", "raw_value": "1725345102.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-5", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 5, "time_seconds": 30.856541633605957, "inputs": {"input_file": {"src": "hda", "id": "46c327a6d434e72f"}, "input_type": "illumina", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "abad5501dcd12988", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:32:12.057026", "update_time": "2024-09-03T06:32:24.758224", "galaxy_version": "24.1", "external_id": "gxy-2962d", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/6/b/1/dataset_6b1e972f-a41e-46ef-8dcd-6aaffc7e7e51.dat' illumina '/galaxy/server/database/objects/a/6/f/dataset_a6f1559e-fec2-4f88-a11e-9e46bb62a69d.dat' sanger ascii summarize_input", "user_email": "tests@fake.org", "command_version": "", "params": {"input_type": "\"illumina\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "46c327a6d434e72f", "src": "hda", "uuid": "6b1e972f-a41e-46ef-8dcd-6aaffc7e7e51"}}, "outputs": {"output_file": {"id": "abad5501dcd12988", "src": "hda", "uuid": "a6f1559e-fec2-4f88-a11e-9e46bb62a69d"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Groomed 2 illumina reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Groomed 2 illumina reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:32:13", "plugin": "core", "name": "start_epoch", "raw_value": "1725345133.0000000"}, {"title": "Job End Time", "value": "2024-09-03 06:32:13", "plugin": "core", "name": "end_epoch", "raw_value": "1725345133.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-6", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 6, "time_seconds": 31.4990451335907, "inputs": {"input_file": {"src": "hda", "id": "cf4925c22d908ffb"}, "input_type": "solexa", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "c897c618250cf7d5", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:32:43.308928", "update_time": "2024-09-03T06:32:56.244021", "galaxy_version": "24.1", "external_id": "gxy-rsmtj", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/a/8/0/dataset_a80cdb30-ddfb-46c7-ab25-c6dadb54ea8c.dat' solexa '/galaxy/server/database/objects/5/1/c/dataset_51c059e8-550b-407b-a59c-c17d8b5acf87.dat' sanger ascii summarize_input", "user_email": "tests@fake.org", "command_version": "", "params": {"input_type": "\"solexa\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "cf4925c22d908ffb", "src": 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"c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:33:14.676772", "update_time": "2024-09-03T06:33:27.432694", "galaxy_version": "24.1", "external_id": "gxy-pvrtl", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/6/2/c/dataset_62ca17a8-eff0-4d23-bbcd-5bc03aa86779.dat' sanger '/galaxy/server/database/objects/2/b/4/dataset_2b4e232a-f34a-40a5-9950-ba0c67ef33ba.dat' sanger ascii summarize_input", "user_email": "tests@fake.org", "command_version": "", "params": {"input_type": "\"sanger\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "10ea677b4495a336", "src": "hda", "uuid": "62ca17a8-eff0-4d23-bbcd-5bc03aa86779"}}, "outputs": {"output_file": {"id": "c18be95c05ac52c6", "src": "hda", "uuid": "2b4e232a-f34a-40a5-9950-ba0c67ef33ba"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 31 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 31 - 93\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:33:16", "plugin": "core", "name": "start_epoch", "raw_value": "1725345196.0000000"}, {"title": "Job End Time", "value": "2024-09-03 06:33:16", "plugin": "core", "name": "end_epoch", "raw_value": "1725345196.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-8", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 8, "time_seconds": 10.780974388122559, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "fastq_groomer/1.1.5-9", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 9, "time_seconds": 30.621323108673096, "inputs": {"input_file": {"src": "hda", "id": "4116c1de5a40792c"}, "input_type": "illumina", "options_type|output_type": "sanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "e5e8cd249a50a76f", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:33:57.119853", "update_time": "2024-09-03T06:34:08.995785", "galaxy_version": "24.1", "external_id": "gxy-rl95n", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/a/f/6/dataset_af6ad6c0-fd93-4118-91cc-36452e80f696.dat' illumina '/galaxy/server/database/objects/4/1/a/dataset_41a6ab6d-a3b9-4fb6-a7c1-ebe1d3c3bfcd.dat' sanger None summarize_input --fix-id", "user_email": "tests@fake.org", "command_version": "", "params": {"input_type": "\"illumina\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "4116c1de5a40792c", "src": "hda", "uuid": "af6ad6c0-fd93-4118-91cc-36452e80f696"}}, "outputs": {"output_file": {"id": "e5e8cd249a50a76f", "src": "hda", "uuid": "41a6ab6d-a3b9-4fb6-a7c1-ebe1d3c3bfcd"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Groomed 2 illumina reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Groomed 2 illumina reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:33:58", "plugin": "core", "name": "end_epoch", "raw_value": "1725345238.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:33:58", "plugin": "core", "name": "start_epoch", "raw_value": "1725345238.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "kallisto_pseudo/0.46.0.1-0", "has_data": true, "data": {"tool_id": "kallisto_pseudo", "tool_version": "0.46.0.1", "test_index": 0, "time_seconds": 44.582236528396606, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "719c08d1fd5e19d9"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|collection|fastq_umi|forward": {"src": "hda", "id": "dede191f31b35b16"}, "single_paired|collection|fastq_umi|reverse": {"src": "hda", "id": "6971d7c8b89d5c6b"}, "single_paired|collection|fastq_umi|umi": "yes", "single_paired|collection|collection_selector": "datasets", "single_paired|single_paired_selector": "paired"}, "job": {"model_class": "Job", "id": "753189cec15eb097", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:49:43.817587", "update_time": "2024-09-03T06:49:59.062300", "galaxy_version": "24.1", "external_id": "gxy-dfq4f", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/2/0/8/dataset_20841d69-45c2-45c8-9f0b-e233b86dd4d1.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . --batch '/galaxy/server/database/jobs_directory/000/91/configs/tmplixzjma7' --umi && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "single_paired": "{\"__current_case__\": 1, \"collection\": {\"__current_case__\": 0, \"collection_selector\": \"datasets\", \"fastq_umi\": {\"__current_case__\": 0, \"forward\": {\"values\": [{\"id\": 93, \"src\": \"hda\"}]}, \"reverse\": {\"values\": [{\"id\": 94, \"src\": \"hda\"}]}, \"umi\": \"yes\"}}, \"single_paired_selector\": \"paired\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 92, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "719c08d1fd5e19d9", "src": "hda", "uuid": "20841d69-45c2-45c8-9f0b-e233b86dd4d1"}, "single_paired|collection|fastq_umi|forward": {"id": "dede191f31b35b16", "src": "hda", "uuid": "b99f2814-b84f-4a2a-9f92-60b441ebd20a"}, "single_paired|collection|fastq_umi|forward1": {"id": "dede191f31b35b16", "src": "hda", "uuid": "b99f2814-b84f-4a2a-9f92-60b441ebd20a"}, "single_paired|collection|fastq_umi|reverse": {"id": "6971d7c8b89d5c6b", "src": "hda", "uuid": "19c1f94b-8f2b-4657-b321-f16c7e9248e3"}, "single_paired|collection|fastq_umi|reverse1": {"id": "6971d7c8b89d5c6b", "src": "hda", "uuid": "19c1f94b-8f2b-4657-b321-f16c7e9248e3"}}, "outputs": {"sample": {"id": "6309df503cee46e6", "src": "hda", "uuid": "7f4ef8a8-b0ff-4893-a5d4-2cecaf33bce0"}, "__new_primary_file_sample|Matrix.cells__": {"id": "e9c083b9bba3a16c", "src": "hda", "uuid": "2f9a0594-3fed-44aa-8c8e-f13ecd5211a7"}, "__new_primary_file_sample|Matrix.ec__": {"id": "3b20e8b159979ec4", "src": "hda", "uuid": "5d16a958-1700-4068-bb6a-625ba5ef97a4"}, "__new_primary_file_sample|Matrix.tabular__": {"id": "63dec8c7c1ecfeb2", "src": "hda", "uuid": "ea7f2637-5881-40f6-9a04-ca4af002d902"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 200,\n\t\"n_pseudoaligned\": 200,\n\t\"n_unique\": 200,\n\t\"p_pseudoaligned\": 100.0,\n\t\"p_unique\": 100.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Sep 3 06:49:48 2024\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . --batch /galaxy/server/database/jobs_directory/000/91/configs/tmplixzjma7 --umi\"\n}\n", "tool_stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in single-end mode\n[quant] will process file 1: /galaxy/server/database/objects/1/9/c/dataset_19c1f94b-8f2b-4657-b321-f16c7e9248e3.dat\n[quant] will process file 1: /galaxy/server/database/objects/1/9/c/dataset_19c1f94b-8f2b-4657-b321-f16c7e9248e3.dat\n[quant] finding pseudoalignments for all files ... done\n[quant] processed 200 reads, 200 reads pseudoaligned, 200 unique UMIs mapped\n\n", "job_stdout": "", "job_stderr": "", "stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 200,\n\t\"n_pseudoaligned\": 200,\n\t\"n_unique\": 200,\n\t\"p_pseudoaligned\": 100.0,\n\t\"p_unique\": 100.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Sep 3 06:49:48 2024\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . --batch /galaxy/server/database/jobs_directory/000/91/configs/tmplixzjma7 --umi\"\n}\n", "stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in single-end mode\n[quant] will process file 1: /galaxy/server/database/objects/1/9/c/dataset_19c1f94b-8f2b-4657-b321-f16c7e9248e3.dat\n[quant] will process file 1: /galaxy/server/database/objects/1/9/c/dataset_19c1f94b-8f2b-4657-b321-f16c7e9248e3.dat\n[quant] finding pseudoalignments for all files ... done\n[quant] processed 200 reads, 200 reads pseudoaligned, 200 unique UMIs mapped\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:49:48", "plugin": "core", "name": "end_epoch", "raw_value": "1725346188.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:49:48", "plugin": "core", "name": "start_epoch", "raw_value": "1725346188.0000000"}, {"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": "kallisto_pseudo/0.46.0.1-1", "has_data": true, "data": {"tool_id": "kallisto_pseudo", "tool_version": "0.46.0.1", "test_index": 1, "time_seconds": 37.530909061431885, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "1a268d8515d4fb32"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|collection|reads": {"src": "hdca", "id": "c5fe43971bba42f1"}, "single_paired|collection|collection_selector": "collection", "single_paired|single_paired_selector": "paired"}, "job": {"model_class": "Job", "id": "6309df503cee46e6", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:50:29.578246", "update_time": "2024-09-03T06:50:42.104492", "galaxy_version": "24.1", "external_id": "gxy-5dpdj", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/d/b/0/dataset_db05ff2a-ca84-44e4-a884-88de30814045.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . '/galaxy/server/database/objects/f/5/b/dataset_f5b5a17e-5ca4-48d8-a4e5-448142357b8e.dat' '/galaxy/server/database/objects/3/5/1/dataset_351c7ba6-9bc9-4213-80e3-6bf7d2d5acfd.dat' && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "single_paired": "{\"__current_case__\": 1, \"collection\": {\"__current_case__\": 1, \"collection_selector\": \"collection\", \"reads\": {\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}}, \"single_paired_selector\": \"paired\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 99, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "1a268d8515d4fb32", "src": "hda", "uuid": "db05ff2a-ca84-44e4-a884-88de30814045"}, "single_paired|collection|reads1": {"id": "dc75f130cdec8859", "src": "hda", "uuid": "f5b5a17e-5ca4-48d8-a4e5-448142357b8e"}, "single_paired|collection|reads2": {"id": "268d30ffb770829a", "src": "hda", "uuid": "351c7ba6-9bc9-4213-80e3-6bf7d2d5acfd"}}, "outputs": {"sample": {"id": "90f9e45a27f92fed", "src": "hda", "uuid": "d45a4278-d182-4c32-bfbe-e579dbbc6197"}, "__new_primary_file_sample|Matrix.cells__": {"id": "a17c4c211de935bf", "src": "hda", "uuid": "ddb59f4a-15a5-4aab-b530-2cd8b5d49b00"}, "__new_primary_file_sample|Matrix.ec__": {"id": "126b74d01ab25540", "src": "hda", "uuid": "778f7a56-93bc-4632-95c9-874db7b63baf"}, "__new_primary_file_sample|Matrix.tabular__": {"id": "f422d8c3699c8315", "src": "hda", "uuid": "202328f0-9a27-410c-a607-9693a22ac4b9"}, "__new_primary_file_sample|Pseudoalignments.ec__": {"id": "1b386e010a78b119", "src": "hda", "uuid": "86f3d5bf-145b-4ded-90ea-2b528d16de7b"}, "__new_primary_file_sample|Pseudoalignments.tabular__": {"id": "101b56dd69096d11", "src": "hda", "uuid": "28acefca-867c-4d5d-a0da-3498033b5673"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 100,\n\t\"n_pseudoaligned\": 0,\n\t\"n_unique\": 0,\n\t\"p_pseudoaligned\": 0.0,\n\t\"p_unique\": 0.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Sep 3 06:50:30 2024\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . /galaxy/server/database/objects/f/5/b/dataset_f5b5a17e-5ca4-48d8-a4e5-448142357b8e.dat /galaxy/server/database/objects/3/5/1/dataset_351c7ba6-9bc9-4213-80e3-6bf7d2d5acfd.dat\"\n}\n", "tool_stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/f/5/b/dataset_f5b5a17e-5ca4-48d8-a4e5-448142357b8e.dat\n /galaxy/server/database/objects/3/5/1/dataset_351c7ba6-9bc9-4213-80e3-6bf7d2d5acfd.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 100 reads, 100 reads pseudoaligned\n\n", "job_stdout": "", "job_stderr": "", "stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 100,\n\t\"n_pseudoaligned\": 0,\n\t\"n_unique\": 0,\n\t\"p_pseudoaligned\": 0.0,\n\t\"p_unique\": 0.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Sep 3 06:50:30 2024\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . /galaxy/server/database/objects/f/5/b/dataset_f5b5a17e-5ca4-48d8-a4e5-448142357b8e.dat /galaxy/server/database/objects/3/5/1/dataset_351c7ba6-9bc9-4213-80e3-6bf7d2d5acfd.dat\"\n}\n", "stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/f/5/b/dataset_f5b5a17e-5ca4-48d8-a4e5-448142357b8e.dat\n /galaxy/server/database/objects/3/5/1/dataset_351c7ba6-9bc9-4213-80e3-6bf7d2d5acfd.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 100 reads, 100 reads pseudoaligned\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:50:30", "plugin": "core", "name": "end_epoch", "raw_value": "1725346230.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:50:30", "plugin": "core", "name": "start_epoch", "raw_value": "1725346230.0000000"}, {"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": "kallisto_pseudo/0.46.0.1-2", "has_data": true, "data": {"tool_id": "kallisto_pseudo", "tool_version": "0.46.0.1", "test_index": 2, "time_seconds": 32.50237488746643, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "299b1d8b8909ae62"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|reads": {"src": "hda", "id": "a605a831a031645f"}, "single_paired|single_paired_selector": "single"}, "job": {"model_class": "Job", "id": "63dec8c7c1ecfeb2", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:51:01.850616", "update_time": "2024-09-03T06:51:14.720089", "galaxy_version": "24.1", "external_id": "gxy-snxts", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/c/e/e/dataset_cee4f51e-5244-472f-ab51-5622f9174f53.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . --single --fragment-length 200 --sd 20 '/galaxy/server/database/objects/3/b/3/dataset_3b3b7702-1a14-43f1-a1e4-2c60dee8c3c9.dat' && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "single_paired": "{\"__current_case__\": 0, \"fragment_length\": \"200\", \"reads\": {\"values\": [{\"id\": 109, \"src\": \"hda\"}]}, \"sd\": \"20\", \"single_paired_selector\": \"single\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 108, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "299b1d8b8909ae62", "src": "hda", "uuid": "cee4f51e-5244-472f-ab51-5622f9174f53"}, "single_paired|reads": {"id": "a605a831a031645f", "src": "hda", "uuid": "3b3b7702-1a14-43f1-a1e4-2c60dee8c3c9"}, "single_paired|reads1": {"id": "a605a831a031645f", "src": "hda", "uuid": "3b3b7702-1a14-43f1-a1e4-2c60dee8c3c9"}}, "outputs": {"sample": {"id": "e5bbc2df36210b85", "src": "hda", "uuid": "059086d2-f687-452c-aa1e-7fa3198c80b6"}, "__new_primary_file_sample|Matrix.cells__": {"id": "9289a2d1390a23f3", "src": "hda", "uuid": "53734d75-3161-4189-b796-454592d90903"}, "__new_primary_file_sample|Matrix.ec__": {"id": "862aea799b88fbcb", "src": "hda", "uuid": "d104b735-02cb-448b-a41f-b77c5432545c"}, "__new_primary_file_sample|Matrix.tabular__": {"id": "3316eddaf4251de1", "src": "hda", "uuid": "4542a3b9-20e0-48de-8cb6-1d4c2fcebc8e"}, "__new_primary_file_sample|Pseudoalignments.ec__": {"id": "ddaa30e73593b3e5", "src": "hda", "uuid": "c263e96a-272b-4324-9882-663fe0426ab5"}, "__new_primary_file_sample|Pseudoalignments.tabular__": {"id": "d3313b4961f32071", "src": "hda", "uuid": "2049c9a3-e76b-4228-99eb-1dce5047f4dc"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 100,\n\t\"n_pseudoaligned\": 0,\n\t\"n_unique\": 0,\n\t\"p_pseudoaligned\": 0.0,\n\t\"p_unique\": 0.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Sep 3 06:51:03 2024\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . --single --fragment-length 200 --sd 20 /galaxy/server/database/objects/3/b/3/dataset_3b3b7702-1a14-43f1-a1e4-2c60dee8c3c9.dat\"\n}\n", "tool_stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in single-end mode\n[quant] will process file 1: /galaxy/server/database/objects/3/b/3/dataset_3b3b7702-1a14-43f1-a1e4-2c60dee8c3c9.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 100 reads, 100 reads pseudoaligned\n\n", "job_stdout": "", "job_stderr": "", "stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 100,\n\t\"n_pseudoaligned\": 0,\n\t\"n_unique\": 0,\n\t\"p_pseudoaligned\": 0.0,\n\t\"p_unique\": 0.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Sep 3 06:51:03 2024\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . --single --fragment-length 200 --sd 20 /galaxy/server/database/objects/3/b/3/dataset_3b3b7702-1a14-43f1-a1e4-2c60dee8c3c9.dat\"\n}\n", "stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in single-end mode\n[quant] will process file 1: /galaxy/server/database/objects/3/b/3/dataset_3b3b7702-1a14-43f1-a1e4-2c60dee8c3c9.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 100 reads, 100 reads pseudoaligned\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:51:03", "plugin": "core", "name": "end_epoch", "raw_value": "1725346263.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:51:03", "plugin": "core", "name": "start_epoch", "raw_value": "1725346263.0000000"}, {"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": "kallisto_pseudo/0.46.0.1-3", "has_data": true, "data": {"tool_id": "kallisto_pseudo", "tool_version": "0.46.0.1", "test_index": 3, "time_seconds": 36.362956047058105, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "4a45112de13adf14"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|collection|fastq_umi|forward": {"src": "hda", "id": "d1834105c588e444"}, "single_paired|collection|fastq_umi|reverse": {"src": "hda", "id": "cbf3c808415d120d"}, "single_paired|collection|fastq_umi|umi": "no", "single_paired|collection|collection_selector": "datasets", "single_paired|single_paired_selector": "paired"}, "job": {"model_class": "Job", "id": "90f9e45a27f92fed", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:51:38.648307", "update_time": "2024-09-03T06:51:51.375946", "galaxy_version": "24.1", "external_id": "gxy-fkxpc", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/4/e/c/dataset_4ecc3370-657d-4bce-9ffc-e782456005e0.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto pseudo -i 'reference.kallisto' --threads ${GALAXY_SLOTS:-1} -o . '/galaxy/server/database/objects/a/f/0/dataset_af02b0d6-f8d9-4fe6-8dca-f1ec2f021123.dat' '/galaxy/server/database/objects/a/4/9/dataset_a49ab179-6cd5-49cf-ad79-3281eb33819e.dat' && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "single_paired": "{\"__current_case__\": 1, \"collection\": {\"__current_case__\": 0, \"collection_selector\": \"datasets\", \"fastq_umi\": {\"__current_case__\": 1, \"forward\": {\"values\": [{\"id\": 117, \"src\": \"hda\"}]}, \"reverse\": {\"values\": [{\"id\": 118, \"src\": \"hda\"}]}, \"umi\": \"no\"}}, \"single_paired_selector\": \"paired\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 116, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "4a45112de13adf14", "src": "hda", "uuid": "4ecc3370-657d-4bce-9ffc-e782456005e0"}, "single_paired|collection|fastq_umi|forward": {"id": "d1834105c588e444", "src": "hda", "uuid": "af02b0d6-f8d9-4fe6-8dca-f1ec2f021123"}, "single_paired|collection|fastq_umi|forward1": {"id": "d1834105c588e444", "src": "hda", "uuid": "af02b0d6-f8d9-4fe6-8dca-f1ec2f021123"}, "single_paired|collection|fastq_umi|reverse": {"id": "cbf3c808415d120d", "src": "hda", "uuid": "a49ab179-6cd5-49cf-ad79-3281eb33819e"}, "single_paired|collection|fastq_umi|reverse1": {"id": "cbf3c808415d120d", "src": "hda", "uuid": "a49ab179-6cd5-49cf-ad79-3281eb33819e"}}, "outputs": {"sample": {"id": "5af00f33c55c183a", "src": "hda", "uuid": "13c1d12e-2768-440b-912b-ab13dca130f8"}, "__new_primary_file_sample|Matrix.cells__": {"id": "48da646b01255f7e", "src": "hda", "uuid": "c12df080-6970-40eb-be0b-66affc24d439"}, "__new_primary_file_sample|Matrix.ec__": {"id": "cbcc5d5ae36a8e0d", "src": "hda", "uuid": "fab6fa56-cefb-4d00-8b52-db4a9a2f51c2"}, "__new_primary_file_sample|Matrix.tabular__": {"id": "67ce37012055eb04", "src": "hda", "uuid": "8bc07432-a991-4ad9-954c-ba675b3a471e"}, "__new_primary_file_sample|Pseudoalignments.ec__": {"id": "1b76baa431b0b231", "src": "hda", "uuid": "cd234046-5c06-48d5-8be6-8397b3903e9f"}, "__new_primary_file_sample|Pseudoalignments.tabular__": {"id": "5b57a0ab1389de76", "src": "hda", "uuid": "960de793-144f-427d-ab41-0869ec2e59ed"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 200,\n\t\"n_pseudoaligned\": 0,\n\t\"n_unique\": 0,\n\t\"p_pseudoaligned\": 0.0,\n\t\"p_unique\": 0.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Sep 3 06:51:40 2024\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . /galaxy/server/database/objects/a/f/0/dataset_af02b0d6-f8d9-4fe6-8dca-f1ec2f021123.dat /galaxy/server/database/objects/a/4/9/dataset_a49ab179-6cd5-49cf-ad79-3281eb33819e.dat\"\n}\n", "tool_stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 15 contigs and contains 16670 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,670\n[index] number of equivalence classes: 1\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/a/f/0/dataset_af02b0d6-f8d9-4fe6-8dca-f1ec2f021123.dat\n /galaxy/server/database/objects/a/4/9/dataset_a49ab179-6cd5-49cf-ad79-3281eb33819e.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 200 reads, 200 reads pseudoaligned\n\n", "job_stdout": "", "job_stderr": "", "stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 200,\n\t\"n_pseudoaligned\": 0,\n\t\"n_unique\": 0,\n\t\"p_pseudoaligned\": 0.0,\n\t\"p_unique\": 0.0,\n\t\"kallisto_version\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Sep 3 06:51:40 2024\",\n\t\"call\": \"kallisto pseudo -i reference.kallisto --threads 1 -o . /galaxy/server/database/objects/a/f/0/dataset_af02b0d6-f8d9-4fe6-8dca-f1ec2f021123.dat /galaxy/server/database/objects/a/4/9/dataset_a49ab179-6cd5-49cf-ad79-3281eb33819e.dat\"\n}\n", "stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 15 contigs and contains 16670 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,670\n[index] number of equivalence classes: 1\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/a/f/0/dataset_af02b0d6-f8d9-4fe6-8dca-f1ec2f021123.dat\n /galaxy/server/database/objects/a/4/9/dataset_a49ab179-6cd5-49cf-ad79-3281eb33819e.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 200 reads, 200 reads pseudoaligned\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:51:40", "plugin": "core", "name": "end_epoch", "raw_value": "1725346300.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:51:40", "plugin": "core", "name": "start_epoch", "raw_value": "1725346300.0000000"}, {"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": "kallisto_pseudo/0.46.0.1-4", "has_data": true, "data": {"tool_id": "kallisto_pseudo", "tool_version": "0.46.0.1", "test_index": 4, "time_seconds": 18.892643928527832, "inputs": {"single_paired|collection|fastq_umi|forward": {"src": "hda", "id": "bed5eec7bbeb2165"}, "single_paired|collection|fastq_umi|reverse": {"src": "hda", "id": "731c4dc86177d504"}, "single_paired|collection|fastq_umi|umi": "yes", "single_paired|collection|collection_selector": "datasets", "single_paired|single_paired_selector": "paired"}, "execution_problem": "parameter 'index': an invalid option (None) was selected, please verify", "dynamic_param_error": true, "status": "error"}}, {"id": "miniasm/0.3+galaxy0-0", "has_data": true, "data": {"tool_id": "miniasm", "tool_version": "0.3+galaxy0", "test_index": 0, "time_seconds": 71.21143174171448, "inputs": {"readFile": {"src": "hda", "id": "c5fe43971bba42f1"}, "paf": {"src": "hda", "id": "a80664568881873a"}}, "job": {"model_class": "Job", "id": "b8ae0f015a2e06aa", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:26:43.190775", "update_time": "2024-09-03T06:27:20.692623", "galaxy_version": "24.1", "external_id": "gxy-xfwpj", "handler": null, "job_runner_name": null, "command_line": "miniasm -f '/galaxy/server/database/objects/0/b/a/dataset_0ba5d077-2fd3-4d97-8b5b-a34154168183.dat' -m '100' -i '0.05' -s '1000' -c '3' -o '1000' -h '1000' -I '0.08' -g '1000' -d '50000' -e '4' -n '3' -F '0.8' '/galaxy/server/database/objects/9/5/d/dataset_95da33ab-f618-4e90-9816-59b7efabc33c.dat' > '/galaxy/server/database/objects/1/1/0/dataset_11078dd4-bda0-4ef4-b2d9-afcf16426295.dat'", "user_email": "tests@fake.org", "command_version": "0.3-r179", "params": {"__input_ext": "\"fastqsanger\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "graph": "{\"finalDropRatio\": \"0.8\", \"maxBubDist\": \"50000\", \"maxGapDiff\": \"1000\", \"minUtgSize\": \"4\", \"nRounds\": \"3\"}", "overlapping": "{\"intThres\": \"0.08\", \"maxHang\": \"1000\", \"minOvlp\": \"1000\"}", "preselection": "{\"minCov\": \"3\", \"minIden\": \"0.05\", \"minMatch\": \"100\", \"minSpan\": \"1000\"}"}, "inputs": {"paf": {"id": "a80664568881873a", "src": "hda", "uuid": "95da33ab-f618-4e90-9816-59b7efabc33c"}, "readFile": {"id": "c5fe43971bba42f1", "src": "hda", "uuid": "0ba5d077-2fd3-4d97-8b5b-a34154168183"}}, "outputs": {"gfa": {"id": "b8ae0f015a2e06aa", "src": "hda", "uuid": "11078dd4-bda0-4ef4-b2d9-afcf16426295"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[M::main] ===> Step 1: reading read mappings <===\n[M::ma_hit_read::0.150*1.00] read 100000 hits; stored 187742 hits and 12067 sequences (111354001 bp)\n[M::main] ===> Step 2: 1-pass (crude) read selection <===\n[M::ma_hit_sub::0.170*1.00] 9155 query sequences remain after sub\n[M::ma_hit_cut::0.175*1.00] 161122 hits remain after cut\n[M::ma_hit_flt::0.177*1.00] 156936 hits remain after filtering; crude coverage after filtering: 11.85\n[M::main] ===> Step 3: 2-pass (fine) read selection <===\n[M::ma_hit_sub::0.187*1.00] 9023 query sequences remain after sub\n[M::ma_hit_cut::0.188*1.00] 152071 hits remain after cut\n[M::ma_hit_contained::0.192*1.00] 1536 sequences and 8359 hits remain after containment removal\n[M::main] ===> Step 4: graph cleaning <===\n[M::ma_sg_gen] read 8236 arcs\n[M::main] ===> Step 4.1: transitive reduction <===\n[M::asg_arc_del_trans] transitively reduced 4182 arcs\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 362 asymmetric arcs\n[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===\n[M::asg_cut_tip] cut 260 tips\n[M::asg_pop_bubble] popped 105 bubbles and trimmed 4 tips\n[M::main] ===> Step 4.3: cutting short overlaps (3 rounds in total) <===\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 29 asymmetric arcs\n[M::asg_arc_del_short] removed 37 short overlaps\n[M::asg_cut_tip] cut 104 tips\n[M::asg_pop_bubble] popped 1 bubbles and trimmed 0 tips\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 1 asymmetric arcs\n[M::asg_arc_del_short] removed 1 short overlaps\n[M::asg_cut_tip] cut 3 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::asg_arc_del_short] removed 0 short overlaps\n[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===\n[M::asg_cut_internal] cut 0 internal sequences\n[M::asg_cut_biloop] cut 0 small bi-loops\n[M::asg_cut_tip] cut 0 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::main] ===> Step 4.5: aggressively cutting short overlaps <===\n[M::asg_arc_del_short] removed 0 short overlaps\n[M::main] ===> Step 5: generating unitigs <===\n[M::main] Version: 0.3-r179\n[M::main] CMD: miniasm -f /galaxy/server/database/objects/0/b/a/dataset_0ba5d077-2fd3-4d97-8b5b-a34154168183.dat -m 100 -i 0.05 -s 1000 -c 3 -o 1000 -h 1000 -I 0.08 -g 1000 -d 50000 -e 4 -n 3 -F 0.8 /galaxy/server/database/objects/9/5/d/dataset_95da33ab-f618-4e90-9816-59b7efabc33c.dat\n[M::main] Real time: 0.203 sec; CPU: 0.201 sec\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[M::main] ===> Step 1: reading read mappings <===\n[M::ma_hit_read::0.150*1.00] read 100000 hits; stored 187742 hits and 12067 sequences (111354001 bp)\n[M::main] ===> Step 2: 1-pass (crude) read selection <===\n[M::ma_hit_sub::0.170*1.00] 9155 query sequences remain after sub\n[M::ma_hit_cut::0.175*1.00] 161122 hits remain after cut\n[M::ma_hit_flt::0.177*1.00] 156936 hits remain after filtering; crude coverage after filtering: 11.85\n[M::main] ===> Step 3: 2-pass (fine) read selection <===\n[M::ma_hit_sub::0.187*1.00] 9023 query sequences remain after sub\n[M::ma_hit_cut::0.188*1.00] 152071 hits remain after cut\n[M::ma_hit_contained::0.192*1.00] 1536 sequences and 8359 hits remain after containment removal\n[M::main] ===> Step 4: graph cleaning <===\n[M::ma_sg_gen] read 8236 arcs\n[M::main] ===> Step 4.1: transitive reduction <===\n[M::asg_arc_del_trans] transitively reduced 4182 arcs\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 362 asymmetric arcs\n[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===\n[M::asg_cut_tip] cut 260 tips\n[M::asg_pop_bubble] popped 105 bubbles and trimmed 4 tips\n[M::main] ===> Step 4.3: cutting short overlaps (3 rounds in total) <===\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 29 asymmetric arcs\n[M::asg_arc_del_short] removed 37 short overlaps\n[M::asg_cut_tip] cut 104 tips\n[M::asg_pop_bubble] popped 1 bubbles and trimmed 0 tips\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 1 asymmetric arcs\n[M::asg_arc_del_short] removed 1 short overlaps\n[M::asg_cut_tip] cut 3 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::asg_arc_del_short] removed 0 short overlaps\n[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===\n[M::asg_cut_internal] cut 0 internal sequences\n[M::asg_cut_biloop] cut 0 small bi-loops\n[M::asg_cut_tip] cut 0 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::main] ===> Step 4.5: aggressively cutting short overlaps <===\n[M::asg_arc_del_short] removed 0 short overlaps\n[M::main] ===> Step 5: generating unitigs <===\n[M::main] Version: 0.3-r179\n[M::main] CMD: miniasm -f /galaxy/server/database/objects/0/b/a/dataset_0ba5d077-2fd3-4d97-8b5b-a34154168183.dat -m 100 -i 0.05 -s 1000 -c 3 -o 1000 -h 1000 -I 0.08 -g 1000 -d 50000 -e 4 -n 3 -F 0.8 /galaxy/server/database/objects/9/5/d/dataset_95da33ab-f618-4e90-9816-59b7efabc33c.dat\n[M::main] Real time: 0.203 sec; CPU: 0.201 sec\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-03 06:27:10", "plugin": "core", "name": "end_epoch", "raw_value": "1725344830.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:27:09", "plugin": "core", "name": "start_epoch", "raw_value": "1725344829.0000000"}, {"title": "Memory Allocated (MB)", "value": "34359", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "34359.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "miniasm/0.3+galaxy0-1", "has_data": true, "data": {"tool_id": "miniasm", "tool_version": "0.3+galaxy0", "test_index": 1, "time_seconds": 32.18396615982056, "inputs": {"readFile": {"src": "hda", "id": "dc997c570f96510e"}, "paf": {"src": "hda", "id": "03b1d146c8da1044"}, "preselection|minMatch": "99", "preselection|minIden": "0.04", "preselection|minSpan": "999", "preselection|minCov": "2", "overlapping|minOvlp": "999", "overlapping|maxHang": "999", "overlapping|intThres": "0.7", "graph|maxGapDiff": "999", "graph|maxBubDist": "45000", "graph|minUtgSize": "3", "graph|nRounds": "2", "graph|finalDropRatio": "0.7"}, "job": {"model_class": "Job", "id": "22f057fa51fff74b", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:27:41.599223", "update_time": "2024-09-03T06:27:53.001050", "galaxy_version": "24.1", "external_id": "gxy-vrzpp", "handler": null, "job_runner_name": null, "command_line": "miniasm -f '/galaxy/server/database/objects/9/7/b/dataset_97b02566-59f7-453e-b759-3f75fa0eab19.dat' -m '99' -i '0.04' -s '999' -c '2' -o '999' -h '999' -I '0.7' -g '999' -d '45000' -e '3' -n '2' -F '0.7' '/galaxy/server/database/objects/4/4/5/dataset_445026e0-dc80-4d1c-95a7-ef2a720e4cfe.dat' > '/galaxy/server/database/objects/6/8/7/dataset_68788490-b501-4324-aad6-a96ec5989fb7.dat'", "user_email": "tests@fake.org", "command_version": "0.3-r179", "params": {"__input_ext": "\"fastqsanger\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "graph": "{\"finalDropRatio\": \"0.7\", \"maxBubDist\": \"45000\", \"maxGapDiff\": \"999\", \"minUtgSize\": \"3\", \"nRounds\": \"2\"}", "overlapping": "{\"intThres\": \"0.7\", \"maxHang\": \"999\", \"minOvlp\": \"999\"}", "preselection": "{\"minCov\": \"2\", \"minIden\": \"0.04\", \"minMatch\": \"99\", \"minSpan\": \"999\"}"}, "inputs": {"paf": {"id": "03b1d146c8da1044", "src": "hda", "uuid": "445026e0-dc80-4d1c-95a7-ef2a720e4cfe"}, "readFile": {"id": "dc997c570f96510e", "src": "hda", "uuid": "97b02566-59f7-453e-b759-3f75fa0eab19"}}, "outputs": {"gfa": {"id": "22f057fa51fff74b", "src": "hda", "uuid": "68788490-b501-4324-aad6-a96ec5989fb7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[M::main] ===> Step 1: reading read mappings <===\n[M::ma_hit_read::0.151*1.00] read 100000 hits; stored 187766 hits and 12068 sequences (111355211 bp)\n[M::main] ===> Step 2: 1-pass (crude) read selection <===\n[M::ma_hit_sub::0.171*1.00] 10122 query sequences remain after sub\n[M::ma_hit_cut::0.173*1.00] 171862 hits remain after cut\n[M::ma_hit_flt::0.175*1.00] 165533 hits remain after filtering; crude coverage after filtering: 11.51\n[M::main] ===> Step 3: 2-pass (fine) read selection <===\n[M::ma_hit_sub::0.186*1.00] 9994 query sequences remain after sub\n[M::ma_hit_cut::0.188*1.00] 163595 hits remain after cut\n[M::ma_hit_contained::0.192*1.00] 1772 sequences and 10061 hits remain after containment removal\n[M::main] ===> Step 4: graph cleaning <===\n[M::ma_sg_gen] read 9758 arcs\n[M::main] ===> Step 4.1: transitive reduction <===\n[M::asg_arc_del_trans] transitively reduced 4694 arcs\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 484 asymmetric arcs\n[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===\n[M::asg_cut_tip] cut 282 tips\n[M::asg_pop_bubble] popped 173 bubbles and trimmed 6 tips\n[M::main] ===> Step 4.3: cutting short overlaps (2 rounds in total) <===\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 26 asymmetric arcs\n[M::asg_arc_del_short] removed 38 short overlaps\n[M::asg_cut_tip] cut 53 tips\n[M::asg_pop_bubble] popped 8 bubbles and trimmed 0 tips\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 2 asymmetric arcs\n[M::asg_arc_del_short] removed 2 short overlaps\n[M::asg_cut_tip] cut 2 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===\n[M::asg_cut_internal] cut 0 internal sequences\n[M::asg_cut_biloop] cut 0 small bi-loops\n[M::asg_cut_tip] cut 0 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::main] ===> Step 4.5: aggressively cutting short overlaps <===\n[M::asg_arc_del_short] removed 0 short overlaps\n[M::main] ===> Step 5: generating unitigs <===\n[M::main] Version: 0.3-r179\n[M::main] CMD: miniasm -f /galaxy/server/database/objects/9/7/b/dataset_97b02566-59f7-453e-b759-3f75fa0eab19.dat -m 99 -i 0.04 -s 999 -c 2 -o 999 -h 999 -I 0.7 -g 999 -d 45000 -e 3 -n 2 -F 0.7 /galaxy/server/database/objects/4/4/5/dataset_445026e0-dc80-4d1c-95a7-ef2a720e4cfe.dat\n[M::main] Real time: 0.206 sec; CPU: 0.205 sec\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[M::main] ===> Step 1: reading read mappings <===\n[M::ma_hit_read::0.151*1.00] read 100000 hits; stored 187766 hits and 12068 sequences (111355211 bp)\n[M::main] ===> Step 2: 1-pass (crude) read selection <===\n[M::ma_hit_sub::0.171*1.00] 10122 query sequences remain after sub\n[M::ma_hit_cut::0.173*1.00] 171862 hits remain after cut\n[M::ma_hit_flt::0.175*1.00] 165533 hits remain after filtering; crude coverage after filtering: 11.51\n[M::main] ===> Step 3: 2-pass (fine) read selection <===\n[M::ma_hit_sub::0.186*1.00] 9994 query sequences remain after sub\n[M::ma_hit_cut::0.188*1.00] 163595 hits remain after cut\n[M::ma_hit_contained::0.192*1.00] 1772 sequences and 10061 hits remain after containment removal\n[M::main] ===> Step 4: graph cleaning <===\n[M::ma_sg_gen] read 9758 arcs\n[M::main] ===> Step 4.1: transitive reduction <===\n[M::asg_arc_del_trans] transitively reduced 4694 arcs\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 484 asymmetric arcs\n[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===\n[M::asg_cut_tip] cut 282 tips\n[M::asg_pop_bubble] popped 173 bubbles and trimmed 6 tips\n[M::main] ===> Step 4.3: cutting short overlaps (2 rounds in total) <===\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 26 asymmetric arcs\n[M::asg_arc_del_short] removed 38 short overlaps\n[M::asg_cut_tip] cut 53 tips\n[M::asg_pop_bubble] popped 8 bubbles and trimmed 0 tips\n[M::asg_arc_del_multi] removed 0 multi-arcs\n[M::asg_arc_del_asymm] removed 2 asymmetric arcs\n[M::asg_arc_del_short] removed 2 short overlaps\n[M::asg_cut_tip] cut 2 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===\n[M::asg_cut_internal] cut 0 internal sequences\n[M::asg_cut_biloop] cut 0 small bi-loops\n[M::asg_cut_tip] cut 0 tips\n[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips\n[M::main] ===> Step 4.5: aggressively cutting short overlaps <===\n[M::asg_arc_del_short] removed 0 short overlaps\n[M::main] ===> Step 5: generating unitigs <===\n[M::main] Version: 0.3-r179\n[M::main] CMD: miniasm -f /galaxy/server/database/objects/9/7/b/dataset_97b02566-59f7-453e-b759-3f75fa0eab19.dat -m 99 -i 0.04 -s 999 -c 2 -o 999 -h 999 -I 0.7 -g 999 -d 45000 -e 3 -n 2 -F 0.7 /galaxy/server/database/objects/4/4/5/dataset_445026e0-dc80-4d1c-95a7-ef2a720e4cfe.dat\n[M::main] Real time: 0.206 sec; CPU: 0.205 sec\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-03 06:27:43", "plugin": "core", "name": "end_epoch", "raw_value": "1725344863.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:27:42", "plugin": "core", "name": "start_epoch", "raw_value": "1725344862.0000000"}, {"title": "Memory Allocated (MB)", "value": "34359", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "34359.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "mummer_mummerplot/4.0.0beta2+galaxy1-0", "has_data": true, "data": {"tool_id": "mummer_mummerplot", "tool_version": "4.0.0beta2+galaxy1", "test_index": 0, "time_seconds": 59.193148136138916, "inputs": {"delta": {"src": "hda", "id": "689616360e4c010a"}, "reference_sequence": {"src": "hda", "id": "f991bfa05ca6802d"}, "query_sequence": {"src": "hda", "id": "953735ae9d7cd0a9"}, "sequences|seq_input": "no", "extra_outs": "all"}, "job": {"model_class": "Job", "id": "25deebca7897c47d", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:47:15.586526", "update_time": "2024-09-03T06:47:48.717504", "galaxy_version": "24.1", "external_id": "gxy-z6ksb", "handler": null, "job_runner_name": null, "command_line": "ln -s /galaxy/server/database/objects/d/5/f/dataset_d5f8bb69-e1d0-41c6-bb90-a1915f73f891.dat reference.fa && ln -s /galaxy/server/database/objects/c/2/d/dataset_c2d07c4b-f9da-4717-9c08-b0aa1effd6b5.dat query.fa && mummerplot -b '20' -s 'small' -terminal png -title 'Title' '/galaxy/server/database/objects/0/d/c/dataset_0dcd2410-b7e5-4fc0-a519-11cb579b069e.dat' && gnuplot < out.gp", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "extra_outs": "\"all\"", "range": "{\"__current_case__\": 1, \"custom\": \"no\"}", "title": "\"Title\"", "snp": "false", "size": "\"small\"", "labels": "{\"IDs\": \"no\", \"__current_case__\": 1}", "fat": "false", "filter": "false", "coverage": "\"\"", "color": "\"\"", "breaklen": "\"20\"", "sequences": "{\"__current_case__\": 1, \"seq_input\": \"no\"}"}, "inputs": {"delta": {"id": "689616360e4c010a", "src": "hda", "uuid": "0dcd2410-b7e5-4fc0-a519-11cb579b069e"}, "reference_sequence": {"id": "f991bfa05ca6802d", "src": "hda", "uuid": "d5f8bb69-e1d0-41c6-bb90-a1915f73f891"}, "query_sequence": {"id": "953735ae9d7cd0a9", "src": "hda", "uuid": "c2d07c4b-f9da-4717-9c08-b0aa1effd6b5"}}, "outputs": {"gnuplot": {"id": "25deebca7897c47d", "src": "hda", "uuid": "86e00b30-a643-437e-8486-f0c0522d9ffe"}, "fplot": {"id": "eaf8e70c10dd6e28", "src": "hda", "uuid": "3b9b5c07-f5e2-4f0e-ab32-90938f11c222"}, "rplot": {"id": "6c8cd3abced55ce4", "src": "hda", "uuid": "e1ae18a3-45d4-4707-8014-66a876589ab0"}, "hplot": {"id": "72ec8975d4ac13fa", "src": "hda", "uuid": "e913752d-b895-4930-8968-63bdcc71d915"}, "output_png": {"id": "07ddd8ef187d4c6f", "src": "hda", "uuid": "0c697ffa-3c9e-4080-9039-c62257f0e4e9"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "gnuplot 5.2 patchlevel 7\n", "tool_stderr": "Reading delta file /galaxy/server/database/objects/0/d/c/dataset_0dcd2410-b7e5-4fc0-a519-11cb579b069e.dat\nWriting plot files out.fplot, out.rplot, out.hplot\nWriting gnuplot script out.gp\nRendering plot out.png\nWARNING: Unable to run 'false out.gp', Inappropriate ioctl for device\n", "job_stdout": "", "job_stderr": "", "stdout": "gnuplot 5.2 patchlevel 7\n", "stderr": "Reading delta file /galaxy/server/database/objects/0/d/c/dataset_0dcd2410-b7e5-4fc0-a519-11cb579b069e.dat\nWriting plot files out.fplot, out.rplot, out.hplot\nWriting gnuplot script out.gp\nRendering plot out.png\nWARNING: Unable to run 'false out.gp', Inappropriate ioctl for device\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:47:31", "plugin": "core", "name": "end_epoch", "raw_value": "1725346051.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:47:31", "plugin": "core", "name": "start_epoch", "raw_value": "1725346051.0000000"}, {"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": "poretools_qualpos/0.6.1a1.1-0", "has_data": true, "data": {"tool_id": "poretools_qualpos", "tool_version": "0.6.1a1.1", "test_index": 0, "time_seconds": 53.698880195617676, "inputs": {"input": {"src": "hda", "id": "bfab2119ff8b913e"}, "extension": "png"}, "job": {"model_class": "Job", "id": "6c8cd3abced55ce4", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:48:09.924779", "update_time": "2024-09-03T06:48:44.804105", "galaxy_version": "24.1", "external_id": "gxy-cv6ms", "handler": null, "job_runner_name": null, "command_line": "export MPLBACKEND=\"agg\" && poretools qualpos '/galaxy/server/database/objects/d/2/f/dataset_d2fec9b0-b293-4776-92c2-29d1d63f9246.dat' --saveas qualpos.png --min-length 0 --max-length 1000000000 --bin-width 1000 && mv qualpos.png '/galaxy/server/database/objects/7/b/6/dataset_7b65c684-a375-4ad2-add9-2d06a1137cf8.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fast5.tar\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "bin_width": "\"1000\"", "max_length": "\"1000000000\"", "min_length": "\"0\"", "theme_bw": "false", "extension": "\"png\""}, "inputs": {"input": {"id": "bfab2119ff8b913e", "src": "hda", "uuid": "d2fec9b0-b293-4776-92c2-29d1d63f9246"}}, "outputs": {"output": {"id": "2e8d1887c71f7a8c", "src": "hda", "uuid": "7b65c684-a375-4ad2-add9-2d06a1137cf8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:poreminion:Processing data...\nINFO:poreminion:Constructing box plot...\nINFO:poreminion:Writing plot to file...\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "INFO:poreminion:Processing data...\nINFO:poreminion:Constructing box plot...\nINFO:poreminion:Writing plot to file...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-03 06:48:27", "plugin": "core", "name": "end_epoch", "raw_value": "1725346107.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:48:25", "plugin": "core", "name": "start_epoch", "raw_value": "1725346105.0000000"}, {"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": "poretools_qualpos/0.6.1a1.1-1", "has_data": true, "data": {"tool_id": "poretools_qualpos", "tool_version": "0.6.1a1.1", "test_index": 1, "time_seconds": 34.59513998031616, "inputs": {"input": {"src": "hda", "id": "080ffbad63804d16"}, "extension": "pdf"}, "job": {"model_class": "Job", "id": "07ddd8ef187d4c6f", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:49:04.543599", "update_time": "2024-09-03T06:49:19.314762", "galaxy_version": "24.1", "external_id": "gxy-fh5d4", "handler": null, "job_runner_name": null, "command_line": "export MPLBACKEND=\"agg\" && poretools qualpos '/galaxy/server/database/objects/8/0/2/dataset_80265725-3d70-4928-be93-db0fceda3fc8.dat' --saveas qualpos.pdf --min-length 0 --max-length 1000000000 --bin-width 1000 && mv qualpos.pdf '/galaxy/server/database/objects/4/9/a/dataset_49aba569-df85-4140-8d2e-73762a5d0fb5.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fast5.tar\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "bin_width": "\"1000\"", "max_length": "\"1000000000\"", "min_length": "\"0\"", "theme_bw": "false", "extension": "\"pdf\""}, "inputs": {"input": {"id": "080ffbad63804d16", "src": "hda", "uuid": "80265725-3d70-4928-be93-db0fceda3fc8"}}, "outputs": {"output": {"id": "753189cec15eb097", "src": "hda", "uuid": "49aba569-df85-4140-8d2e-73762a5d0fb5"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "INFO:poreminion:Processing data...\nINFO:poreminion:Constructing box plot...\nINFO:poreminion:Writing plot to file...\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "INFO:poreminion:Processing data...\nINFO:poreminion:Constructing box plot...\nINFO:poreminion:Writing plot to file...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-03 06:49:08", "plugin": "core", "name": "end_epoch", "raw_value": "1725346148.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:49:06", "plugin": "core", "name": "start_epoch", "raw_value": "1725346146.0000000"}, {"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": "query_tabular/3.3.0-0", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 0, "time_seconds": 37.78534936904907, "inputs": {"tables_0|table": {"src": "hda", "id": 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"sqlquery": "\"SELECT FirstName,LastName,sum(SaleAmount) as \\\"TotalSales\\\" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}]}, \"table\": {\"values\": [{\"id\": 141, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"CustomerID,FirstName,LastName,Email,DOB,Phone\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"customers\"}}, {\"__index__\": 1, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}]}, \"table\": {\"values\": [{\"id\": 142, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"CustomerID,Date,SaleAmount\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"sales\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "b88fe9f6668d305b", "src": "hda", "uuid": "dc00c48c-ea9f-48d2-b764-04f2c1d17455"}, "tables_1|table": {"id": "b1314eb67a4dcd5a", "src": "hda", "uuid": "18b8f8af-00c8-4e1c-82a9-8d3698ebc4e8"}}, "outputs": {"output": {"id": "c56d003b54f034be", "src": "hda", "uuid": "52030cdc-5db4-40ef-a23c-b54abb545198"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\nSELECT FirstName,LastName,sum(SaleAmount) as \"TotalSales\" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/d/c/0/dataset_dc00c48c-ea9f-48d2-b764-04f2c1d17455.dat', 'table_name': 'customers', 'column_names': 'CustomerID,FirstName,LastName,Email,DOB,Phone', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}, {'file_path': '/galaxy/server/database/objects/1/8/b/dataset_18b8f8af-00c8-4e1c-82a9-8d3698ebc4e8.dat', 'table_name': 'sales', 'column_names': 'CustomerID,Date,SaleAmount', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}]}\n\nSQL: \nSELECT FirstName,LastName,sum(SaleAmount) as \"TotalSales\" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stdout": "\nSELECT FirstName,LastName,sum(SaleAmount) as \"TotalSales\" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC\n ", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/d/c/0/dataset_dc00c48c-ea9f-48d2-b764-04f2c1d17455.dat', 'table_name': 'customers', 'column_names': 'CustomerID,FirstName,LastName,Email,DOB,Phone', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}, {'file_path': '/galaxy/server/database/objects/1/8/b/dataset_18b8f8af-00c8-4e1c-82a9-8d3698ebc4e8.dat', 'table_name': 'sales', 'column_names': 'CustomerID,Date,SaleAmount', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}]}\n\nSQL: \nSELECT FirstName,LastName,sum(SaleAmount) as \"TotalSales\" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC\n \nrowcount: None\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-03 06:56:04", "plugin": 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"tables_1|input_opts|linefilters_0|filter|skip_lines": "1", "tables_1|input_opts|linefilters_0|filter|filter_type": "skip", "sqlquery": "SELECT FirstName,LastName,sum(t2.c3) as \"TotalSales\" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;"}, "job": {"model_class": "Job", "id": "67ce37012055eb04", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:56:34.716432", "update_time": "2024-09-03T06:56:47.495312", "galaxy_version": "24.1", "external_id": "gxy-ggtwn", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/122/configs/tmpm9lf6m4t' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/122/configs/tmp6ur0tthu' -Q '/galaxy/server/database/jobs_directory/000/122/configs/tmpm9lf6m4t' --comment_char='#' -o '/galaxy/server/database/objects/0/c/7/dataset_0c77895f-3af5-4f9f-bec2-42f2fb536d37.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"SELECT FirstName,LastName,sum(t2.c3) as \\\"TotalSales\\\" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}]}, \"table\": {\"values\": [{\"id\": 144, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \",FirstName,LastName,,DOB,\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"\"}}, {\"__index__\": 1, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 0, \"filter_type\": \"skip\", \"skip_lines\": \"1\"}}]}, \"table\": {\"values\": [{\"id\": 145, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "97d5fce5154a6645", "src": "hda", "uuid": "db9be421-2bb2-4119-8158-f2d61f86df8b"}, "tables_1|table": {"id": "2841ee9a8ba77b56", "src": "hda", "uuid": "537ac4c1-04d8-4baf-8989-6e0ff7a1ffad"}}, "outputs": {"output": {"id": "cd15ced39043732a", "src": "hda", "uuid": "0c77895f-3af5-4f9f-bec2-42f2fb536d37"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\nSELECT FirstName,LastName,sum(t2.c3) as \"TotalSales\" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/d/b/9/dataset_db9be421-2bb2-4119-8158-f2d61f86df8b.dat', 'table_name': 't1', 'column_names': ',FirstName,LastName,,DOB,', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}, {'file_path': '/galaxy/server/database/objects/5/3/7/dataset_537ac4c1-04d8-4baf-8989-6e0ff7a1ffad.dat', 'table_name': 't2', 'column_names': '', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nSELECT FirstName,LastName,sum(t2.c3) as \"TotalSales\" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stdout": "\nSELECT FirstName,LastName,sum(t2.c3) as \"TotalSales\" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;\n ", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/d/b/9/dataset_db9be421-2bb2-4119-8158-f2d61f86df8b.dat', 'table_name': 't1', 'column_names': ',FirstName,LastName,,DOB,', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}, {'file_path': '/galaxy/server/database/objects/5/3/7/dataset_537ac4c1-04d8-4baf-8989-6e0ff7a1ffad.dat', 'table_name': 't2', 'column_names': '', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nSELECT FirstName,LastName,sum(t2.c3) as \"TotalSales\" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;\n \nrowcount: None\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-03 06:56:37", "plugin": "core", "name": "end_epoch", "raw_value": "1725346597.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:56:36", "plugin": "core", "name": "start_epoch", "raw_value": "1725346596.0000000"}, {"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": "query_tabular/3.3.0-10", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 10, "time_seconds": 31.123493432998657, "inputs": {"tables_0|table": {"src": "hda", "id": "2ec2f6c50a5df2b0"}, "tables_0|input_opts|linefilters_0|filter|regex_pattern": "NOT TO BE FOUND", "tables_0|input_opts|linefilters_0|filter|regex_action": "include_find", "tables_0|input_opts|linefilters_0|filter|filter_type": "regex", "tables_0|tbl_opts|table_name": "epitope", "tables_0|tbl_opts|column_names_from_first_line": false, "tables_0|tbl_opts|col_names": "pos,peptide,logscore,,,,Allele", "sqlquery": "SELECT pos,peptide,logscore,Allele FROM epitope", "query_result|header_prefix": "", "query_result|header": "yes"}, "job": {"model_class": "Job", "id": "b88fe9f6668d305b", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T07:00:39.985086", "update_time": "2024-09-03T07:00:52.665417", "galaxy_version": "24.1", "external_id": "gxy-rd7rk", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/141/configs/tmp8gv777h3' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/141/configs/tmp7zy_0vob' -Q '/galaxy/server/database/jobs_directory/000/141/configs/tmp8gv777h3' -o '/galaxy/server/database/objects/6/d/5/dataset_6d52d198-b4fa-4473-93eb-04bc9b64d44f.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}", "sqlquery": "\"SELECT pos,peptide,logscore,Allele FROM epitope\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"NOT TO BE FOUND\"}}]}, \"table\": {\"values\": [{\"id\": 165, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"pos,peptide,logscore,,,,Allele\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"epitope\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "2ec2f6c50a5df2b0", "src": "hda", "uuid": "bbfd3edd-633e-453b-8844-0557916a7273"}}, "outputs": {"output": {"id": "fde3f8113c3f3a2c", "src": "hda", "uuid": "6d52d198-b4fa-4473-93eb-04bc9b64d44f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\nSELECT pos,peptide,logscore,Allele FROM epitope\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/b/b/f/dataset_bbfd3edd-633e-453b-8844-0557916a7273.dat', 'table_name': 'epitope', 'column_names': 'pos,peptide,logscore,,,,Allele', 'filters': [{'filter': 'regex', 'pattern': 'NOT TO BE FOUND', 'action': 'include_find'}]}]}\n\nSQL: \nSELECT pos,peptide,logscore,Allele FROM epitope\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stdout": "\nSELECT pos,peptide,logscore,Allele FROM epitope\n ", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/b/b/f/dataset_bbfd3edd-633e-453b-8844-0557916a7273.dat', 'table_name': 'epitope', 'column_names': 'pos,peptide,logscore,,,,Allele', 'filters': [{'filter': 'regex', 'pattern': 'NOT TO BE FOUND', 'action': 'include_find'}]}]}\n\nSQL: \nSELECT pos,peptide,logscore,Allele FROM epitope\n \nrowcount: None\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 07:00:42", "plugin": "core", "name": "end_epoch", "raw_value": "1725346842.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 07:00:42", "plugin": "core", "name": "start_epoch", "raw_value": "1725346842.0000000"}, {"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": "query_tabular/3.3.0-11", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 11, "time_seconds": 32.00814461708069, "inputs": {"tables_0|table": {"src": "hda", "id": "3170aee031c22217"}, "sqlquery": "SELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1"}, "job": {"model_class": "Job", "id": "c56d003b54f034be", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T07:01:12.195038", "update_time": "2024-09-03T07:01:24.817291", "galaxy_version": "24.1", "external_id": "gxy-7c7qm", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/143/configs/tmpddpl87a4' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/143/configs/tmpzdi21_fw' -Q '/galaxy/server/database/jobs_directory/000/143/configs/tmpddpl87a4' --comment_char='#' -o '/galaxy/server/database/objects/c/2/e/dataset_c2ee71db-d54d-401c-a0af-fac28dc6e34c.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"SELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": []}, \"table\": {\"values\": [{\"id\": 167, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "3170aee031c22217", "src": "hda", "uuid": "adb7bbec-6945-4a3b-8861-e7b2879da4c8"}}, "outputs": {"output": {"id": "2dfc05ae38b573a5", "src": "hda", "uuid": "c2ee71db-d54d-401c-a0af-fac28dc6e34c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\nSELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/a/d/b/dataset_adb7bbec-6945-4a3b-8861-e7b2879da4c8.dat', 'table_name': 't1', 'column_names': ''}]}\nsqrt(-2): math domain error\nsqrt(-2.222): math domain error\nlog(-2): math domain error\nlog10(-2): math domain error\nacos(-2): math domain error\nasin(-2): math domain error\nacosh(-2): math domain error\nsqrt(-1): math domain error\nsqrt(-1.999): math domain error\nlog(-1): math domain error\nlog10(-1): math domain error\nacosh(-1): math domain error\nlog(0): math domain error\nlog10(0): math domain error\nacosh(0): math domain error\nacos(2): math domain error\nasin(2): math domain error\nacos(3): math domain error\nasin(3): math domain error\nacos(4): math domain error\nasin(4): math domain error\nacos(5): math domain error\nasin(5): math domain error\n\nSQL: \nSELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stdout": "\nSELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\n ", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/a/d/b/dataset_adb7bbec-6945-4a3b-8861-e7b2879da4c8.dat', 'table_name': 't1', 'column_names': ''}]}\nsqrt(-2): math domain error\nsqrt(-2.222): math domain error\nlog(-2): math domain error\nlog10(-2): math domain error\nacos(-2): math domain error\nasin(-2): math domain error\nacosh(-2): math domain error\nsqrt(-1): math domain error\nsqrt(-1.999): math domain error\nlog(-1): math domain error\nlog10(-1): math domain error\nacosh(-1): math domain error\nlog(0): math domain error\nlog10(0): math domain error\nacosh(0): math domain error\nacos(2): math domain error\nasin(2): math domain error\nacos(3): math domain error\nasin(3): math domain error\nacos(4): math domain error\nasin(4): math domain error\nacos(5): math domain error\nasin(5): math domain error\n\nSQL: \nSELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\n \nrowcount: None\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 07:01:13", "plugin": "core", "name": "end_epoch", "raw_value": "1725346873.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 07:01:13", "plugin": "core", "name": "start_epoch", "raw_value": "1725346873.0000000"}, {"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": "query_tabular/3.3.0-2", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 2, "time_seconds": 30.147024154663086, "inputs": {"tables_0|table": {"src": "hda", "id": "3ecfb97d326c16cf"}, "tables_0|input_opts|linefilters_0|filter|skip_lines": "1", "tables_0|input_opts|linefilters_0|filter|filter_type": "skip", "tables_0|tbl_opts|col_names": ",FirstName,LastName,,BirthDate,", "sqlquery": "select FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)"}, "job": {"model_class": "Job", "id": "5b57a0ab1389de76", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:57:05.827696", "update_time": "2024-09-03T06:57:17.681915", "galaxy_version": "24.1", "external_id": "gxy-rnfbc", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/124/configs/tmp1p8bg8a1' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/124/configs/tmpc_vtuxv1' -Q '/galaxy/server/database/jobs_directory/000/124/configs/tmp1p8bg8a1' --comment_char='#' -o '/galaxy/server/database/objects/5/3/5/dataset_5354a852-f6e3-4a2e-b605-fbe1325fc45f.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"select FirstName,LastName,re_sub('^\\\\d{2}(\\\\d{2})-(\\\\d\\\\d)-(\\\\d\\\\d)','\\\\3/\\\\2/\\\\1',BirthDate) as \\\"DOB\\\" from t1 WHERE re_search('[hp]er',c4)\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 0, \"filter_type\": \"skip\", \"skip_lines\": \"1\"}}]}, \"table\": {\"values\": [{\"id\": 147, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \",FirstName,LastName,,BirthDate,\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "3ecfb97d326c16cf", "src": "hda", "uuid": "d18ac2ec-a43f-4d3f-b1ae-f4e57da5f55f"}}, "outputs": {"output": {"id": "c2ead3138e662556", "src": "hda", "uuid": "5354a852-f6e3-4a2e-b605-fbe1325fc45f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\nselect FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/d/1/8/dataset_d18ac2ec-a43f-4d3f-b1ae-f4e57da5f55f.dat', 'table_name': 't1', 'column_names': ',FirstName,LastName,,BirthDate,', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nselect FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stdout": "\nselect FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)\n ", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/d/1/8/dataset_d18ac2ec-a43f-4d3f-b1ae-f4e57da5f55f.dat', 'table_name': 't1', 'column_names': ',FirstName,LastName,,BirthDate,', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nselect FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)\n \nrowcount: None\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:57:07", "plugin": "core", "name": "end_epoch", "raw_value": "1725346627.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:57:07", "plugin": "core", "name": "start_epoch", "raw_value": "1725346627.0000000"}, {"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": "query_tabular/3.3.0-3", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 3, "time_seconds": 32.345369815826416, "inputs": {"tables_0|table": {"src": "hda", "id": "070fd72f262e6305"}, "tables_0|input_opts|linefilters_0|filter|comment_char": "35", "tables_0|input_opts|linefilters_0|filter|filter_type": "comment", "tables_0|tbl_opts|table_name": "iedb", "tables_0|tbl_opts|col_names": "ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank", "tables_1|table": {"src": "hda", "id": "35ff7e90998c8cd2"}, "tables_1|input_opts|linefilters_0|filter|skip_lines": "1", "tables_1|input_opts|linefilters_0|filter|filter_type": "skip", "tables_1|tbl_opts|table_name": "mhc_summary", "tables_1|tbl_opts|col_names": "pos,peptide,logscore,affinity,Bind_Level,Protein,Allele", "sqlquery": "select iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank"}, "job": {"model_class": "Job", "id": "519c268d6e571334", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:57:37.896011", "update_time": "2024-09-03T06:57:50.152654", "galaxy_version": "24.1", "external_id": "gxy-4ngrt", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/127/configs/tmpkeuieg92' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/127/configs/tmpxwc4bz9w' -Q '/galaxy/server/database/jobs_directory/000/127/configs/tmpkeuieg92' --comment_char='#' -o '/galaxy/server/database/objects/9/2/6/dataset_926758ac-b26e-4c97-9032-d068c0fdcf03.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"select iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}]}, \"table\": {\"values\": [{\"id\": 149, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"iedb\"}}, {\"__index__\": 1, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 0, \"filter_type\": \"skip\", \"skip_lines\": \"1\"}}]}, \"table\": {\"values\": [{\"id\": 150, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"pos,peptide,logscore,affinity,Bind_Level,Protein,Allele\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"mhc_summary\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "070fd72f262e6305", "src": "hda", "uuid": "e1f4193a-0d03-4c43-ad07-dcbf6fff57fb"}, "tables_1|table": {"id": "35ff7e90998c8cd2", "src": "hda", "uuid": "bdc547c2-4b29-49ad-a388-035b525609aa"}}, "outputs": {"output": {"id": "d486de5d89b20555", "src": "hda", "uuid": "926758ac-b26e-4c97-9032-d068c0fdcf03"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\nselect iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/e/1/f/dataset_e1f4193a-0d03-4c43-ad07-dcbf6fff57fb.dat', 'table_name': 'iedb', 'column_names': 'ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}, {'file_path': '/galaxy/server/database/objects/b/d/c/dataset_bdc547c2-4b29-49ad-a388-035b525609aa.dat', 'table_name': 'mhc_summary', 'column_names': 'pos,peptide,logscore,affinity,Bind_Level,Protein,Allele', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nselect iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stdout": "\nselect iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\n ", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/e/1/f/dataset_e1f4193a-0d03-4c43-ad07-dcbf6fff57fb.dat', 'table_name': 'iedb', 'column_names': 'ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}, {'file_path': '/galaxy/server/database/objects/b/d/c/dataset_bdc547c2-4b29-49ad-a388-035b525609aa.dat', 'table_name': 'mhc_summary', 'column_names': 'pos,peptide,logscore,affinity,Bind_Level,Protein,Allele', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nselect iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\n \nrowcount: None\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:57:39", "plugin": "core", "name": "end_epoch", "raw_value": "1725346659.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:57:39", "plugin": "core", "name": "start_epoch", "raw_value": "1725346659.0000000"}, {"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": "query_tabular/3.3.0-4", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 4, "time_seconds": 24.2345232963562, "inputs": {"add_to_database|withdb": {"src": "hda", "id": "5cfa2c742a69011a"}, "tables_0|table": {"src": "hda", "id": "b17c5c82cd3ecfce"}, "tables_0|input_opts|linefilters_0|filter|regex_pattern": "^\\d+", "tables_0|input_opts|linefilters_0|filter|regex_action": "include_find", "tables_0|input_opts|linefilters_0|filter|filter_type": "regex", "tables_0|input_opts|linefilters_1|filter|comment_char": "35", "tables_0|input_opts|linefilters_1|filter|filter_type": "comment", "tables_0|input_opts|linefilters_2|filter|filter_type": "append_line_num", "tables_0|input_opts|linefilters_3|filter|columns": "7,2,3,4,1", "tables_0|input_opts|linefilters_3|filter|filter_type": "select_columns", "tables_0|input_opts|linefilters_4|filter|column": "c4", "tables_0|input_opts|linefilters_4|filter|regex_pattern": "(\\d+)/(\\d+)/(\\d+)", "tables_0|input_opts|linefilters_4|filter|regex_replace": "19\\3-\\2-\\1", "tables_0|input_opts|linefilters_4|filter|filter_type": "replace", "tables_0|tbl_opts|table_name": "people", "tables_0|tbl_opts|col_names": "id,first,last,dob,pets", "sqlquery": "SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name"}, "job": {"model_class": "Job", "id": "60dc8ed2ca8581ac", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "state": "error", "exit_code": null, "create_time": "2024-09-03T06:58:10.264162", "update_time": "2024-09-03T06:58:14.627333", "galaxy_version": "24.1", "external_id": "gxy-44j2j", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/130/configs/tmp7_jrxnls' && cp '/galaxy/server/database/objects/e/1/0/dataset_e106e609-955c-4b07-8741-017cc91a020e.dat' 'workdb.sqlite' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/130/configs/tmpy5o6f8gl' -Q '/galaxy/server/database/jobs_directory/000/130/configs/tmp7_jrxnls' --comment_char='#' -o '/galaxy/server/database/objects/8/c/8/dataset_8c882cff-dcfc-4326-b285-ddc57cecc7db.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"sqlite\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"^\\\\d+\"}}, {\"__index__\": 1, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}, {\"__index__\": 2, \"filter\": {\"__current_case__\": 3, \"filter_type\": \"append_line_num\"}}, {\"__index__\": 3, \"filter\": {\"__current_case__\": 9, \"columns\": \"7,2,3,4,1\", \"filter_type\": \"select_columns\"}}, {\"__index__\": 4, \"filter\": {\"__current_case__\": 11, \"add\": null, \"column\": \"c4\", \"filter_type\": \"replace\", \"regex_pattern\": \"(\\\\d+)/(\\\\d+)/(\\\\d+)\", \"regex_replace\": \"19\\\\3-\\\\2-\\\\1\"}}]}, \"table\": {\"values\": [{\"id\": 153, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"id,first,last,dob,pets\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"people\"}}]", "add_to_database": "{\"withdb\": {\"values\": [{\"id\": 152, \"src\": \"hda\"}]}}", "workdb": "\"workdb.sqlite\""}, "inputs": {"add_to_database|withdb": {"id": "5cfa2c742a69011a", "src": "hda", "uuid": "e106e609-955c-4b07-8741-017cc91a020e"}, "tables_0|table": {"id": "b17c5c82cd3ecfce", "src": "hda", "uuid": "b746cd5b-f442-4c12-9a2d-08f780790990"}}, "outputs": {"output": {"id": "ac7f57a7a56a19b0", "src": "hda", "uuid": "8c882cff-dcfc-4326-b285-ddc57cecc7db"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/b/7/4/dataset_b746cd5b-f442-4c12-9a2d-08f780790990.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}]}\n\nSQL: \nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n \nrowcount: None\n", "job_stdout": null, "job_stderr": null, "stdout": "\nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n ", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/b/7/4/dataset_b746cd5b-f442-4c12-9a2d-08f780790990.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}]}\n\nSQL: \nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n \nrowcount: None\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, exit_code: None, stderr: JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/b/7/4/dataset_b746cd5b-f442-4c12-9a2d-08f780790990.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}]}\n\nSQL: \nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n \nrowcount: None\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, exit_code: None, stderr: JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/b/7/4/dataset_b746cd5b-f442-4c12-9a2d-08f780790990.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}]}\n\nSQL: \nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n \nrowcount: None\n."], "status": "failure"}}, {"id": "query_tabular/3.3.0-5", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 5, "time_seconds": 30.380126476287842, "inputs": {"tables_0|table": {"src": "hda", "id": "07bd73e8fa8b74fa"}, "tables_0|input_opts|linefilters_0|filter|regex_pattern": "^\\d+", "tables_0|input_opts|linefilters_0|filter|regex_action": "include_find", "tables_0|input_opts|linefilters_0|filter|filter_type": "regex", "tables_0|input_opts|linefilters_1|filter|comment_char": "35", "tables_0|input_opts|linefilters_1|filter|filter_type": "comment", "tables_0|input_opts|linefilters_2|filter|filter_type": "append_line_num", "tables_0|input_opts|linefilters_3|filter|columns": "7,2,3,4,1", "tables_0|input_opts|linefilters_3|filter|filter_type": "select_columns", "tables_0|input_opts|linefilters_4|filter|column": "c4", "tables_0|input_opts|linefilters_4|filter|regex_pattern": "(\\d+)/(\\d+)/(\\d+)", "tables_0|input_opts|linefilters_4|filter|regex_replace": "19\\3-\\2-\\1", "tables_0|input_opts|linefilters_4|filter|filter_type": "replace", "tables_0|tbl_opts|table_name": "people", "tables_0|tbl_opts|col_names": "id,first,last,dob,pets", "tables_1|table": {"src": "hda", "id": "07bd73e8fa8b74fa"}, "tables_1|input_opts|linefilters_0|filter|regex_pattern": "^\\d+", "tables_1|input_opts|linefilters_0|filter|regex_action": "include_find", "tables_1|input_opts|linefilters_0|filter|filter_type": "regex", "tables_1|input_opts|linefilters_1|filter|filter_type": "append_line_num", "tables_1|input_opts|linefilters_2|filter|columns": "c7,c5,c6", "tables_1|input_opts|linefilters_2|filter|filter_type": "select_columns", "tables_1|input_opts|linefilters_3|filter|columns": "c2,c3", "tables_1|input_opts|linefilters_3|filter|separator": ",", "tables_1|input_opts|linefilters_3|filter|filter_type": "normalize", "tables_1|tbl_opts|table_name": "pet", "tables_1|tbl_opts|col_names": "id,name,animal", "sqlquery": "SELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'"}, "job": {"model_class": "Job", "id": "16409116e0085a10", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:58:32.960231", "update_time": "2024-09-03T06:58:44.819387", "galaxy_version": "24.1", "external_id": "gxy-7p4kk", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/132/configs/tmp0bod44n5' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/132/configs/tmpgwhf4d0r' -Q '/galaxy/server/database/jobs_directory/000/132/configs/tmp0bod44n5' --comment_char='#' -o '/galaxy/server/database/objects/5/c/6/dataset_5c6eb3d3-f175-46cd-b7ea-c4010a5ec942.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"SELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"^\\\\d+\"}}, {\"__index__\": 1, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}, {\"__index__\": 2, \"filter\": {\"__current_case__\": 3, \"filter_type\": \"append_line_num\"}}, {\"__index__\": 3, \"filter\": {\"__current_case__\": 9, \"columns\": \"7,2,3,4,1\", \"filter_type\": \"select_columns\"}}, {\"__index__\": 4, \"filter\": {\"__current_case__\": 11, \"add\": null, \"column\": \"c4\", \"filter_type\": \"replace\", \"regex_pattern\": \"(\\\\d+)/(\\\\d+)/(\\\\d+)\", \"regex_replace\": \"19\\\\3-\\\\2-\\\\1\"}}]}, \"table\": {\"values\": [{\"id\": 155, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"id,first,last,dob,pets\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"people\"}}, {\"__index__\": 1, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"^\\\\d+\"}}, {\"__index__\": 1, \"filter\": {\"__current_case__\": 3, \"filter_type\": \"append_line_num\"}}, {\"__index__\": 2, \"filter\": {\"__current_case__\": 9, \"columns\": \"c7,c5,c6\", \"filter_type\": \"select_columns\"}}, {\"__index__\": 3, \"filter\": {\"__current_case__\": 12, \"columns\": \"c2,c3\", \"filter_type\": \"normalize\", \"separator\": \",\"}}]}, \"table\": {\"values\": [{\"id\": 155, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"id,name,animal\", \"column_names_from_first_line\": false, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"pet\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "07bd73e8fa8b74fa", "src": "hda", "uuid": "f8d22288-095a-4cc8-9820-aba8c04285dc"}, "tables_1|table": {"id": "07bd73e8fa8b74fa", "src": "hda", "uuid": "f8d22288-095a-4cc8-9820-aba8c04285dc"}}, "outputs": {"output": {"id": "ce7e732c31d9ead0", "src": "hda", "uuid": "5c6eb3d3-f175-46cd-b7ea-c4010a5ec942"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\nSELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/f/8/d/dataset_f8d22288-095a-4cc8-9820-aba8c04285dc.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}, {'file_path': '/galaxy/server/database/objects/f/8/d/dataset_f8d22288-095a-4cc8-9820-aba8c04285dc.dat', 'table_name': 'pet', 'column_names': 'id,name,animal', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 5, 6]}, {'filter': 'normalize', 'columns': [2, 3], 'separator': ','}]}]}\n\nSQL: \nSELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stdout": "\nSELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'\n ", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/f/8/d/dataset_f8d22288-095a-4cc8-9820-aba8c04285dc.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}, {'file_path': '/galaxy/server/database/objects/f/8/d/dataset_f8d22288-095a-4cc8-9820-aba8c04285dc.dat', 'table_name': 'pet', 'column_names': 'id,name,animal', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 5, 6]}, {'filter': 'normalize', 'columns': [2, 3], 'separator': ','}]}]}\n\nSQL: \nSELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'\n \nrowcount: None\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:58:34", "plugin": "core", "name": "end_epoch", "raw_value": "1725346714.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:58:34", "plugin": "core", "name": "start_epoch", "raw_value": "1725346714.0000000"}, {"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": "query_tabular/3.3.0-6", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 6, "time_seconds": 31.36926007270813, "inputs": {"tables_0|table": {"src": "hda", "id": "00e9c169862726a9"}, "tables_0|input_opts|linefilters_0|filter|columns": "1,3,2,6,14,19", "tables_0|input_opts|linefilters_0|filter|filter_type": "select_columns", "tables_0|tbl_opts|table_name": "PSMs", "tables_0|tbl_opts|column_names_from_first_line": true, "tables_0|tbl_opts|col_names": "Scan", "sqlquery": "SELECT * from PSMs", "query_result|header_prefix": "", "query_result|header": "yes"}, "job": {"model_class": "Job", "id": "c70250f1936d4dbf", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:59:03.718078", "update_time": "2024-09-03T06:59:16.518436", "galaxy_version": "24.1", "external_id": "gxy-xvfnk", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/134/configs/tmpi69szrgb' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/134/configs/tmpgpj8q8gd' -Q '/galaxy/server/database/jobs_directory/000/134/configs/tmpi69szrgb' -o '/galaxy/server/database/objects/c/e/3/dataset_ce39e522-d6d1-4fb7-b7d6-8f39c5bbb3b3.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}", "sqlquery": "\"SELECT * from PSMs\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 9, \"columns\": \"1,3,2,6,14,19\", \"filter_type\": \"select_columns\"}}]}, \"table\": {\"values\": [{\"id\": 157, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"Scan\", \"column_names_from_first_line\": true, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"PSMs\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "00e9c169862726a9", "src": "hda", "uuid": "fe5df193-4c7d-48cd-8f66-680bb6efd073"}}, "outputs": {"output": {"id": "a03238cf59f59304", "src": "hda", "uuid": "ce39e522-d6d1-4fb7-b7d6-8f39c5bbb3b3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\nSELECT * from PSMs\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/f/e/5/dataset_fe5df193-4c7d-48cd-8f66-680bb6efd073.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'Scan', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19]}]}]}\n\nSQL: \nSELECT * from PSMs\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stdout": "\nSELECT * from PSMs\n ", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/f/e/5/dataset_fe5df193-4c7d-48cd-8f66-680bb6efd073.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'Scan', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19]}]}]}\n\nSQL: \nSELECT * from PSMs\n \nrowcount: None\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:59:05", "plugin": "core", "name": "end_epoch", "raw_value": "1725346745.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:59:05", "plugin": "core", "name": "start_epoch", "raw_value": "1725346745.0000000"}, {"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": "query_tabular/3.3.0-7", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 7, "time_seconds": 10.9267578125, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "query_tabular/3.3.0-8", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 8, "time_seconds": 22.536759853363037, "inputs": {"tables_0|table": {"src": "hda", "id": "f88cf8ee998749f2"}, "tables_0|input_opts|linefilters_0|filter|columns": "1,3,2,6,14,19,23", "tables_0|input_opts|linefilters_0|filter|filter_type": "select_columns", "tables_0|tbl_opts|table_name": "PSMs", "tables_0|tbl_opts|column_names_from_first_line": true, "tables_0|tbl_opts|col_names": "scan,,,,,,confidence", "modify_database|sql_stmts_0|sqlstmt": "UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0", "sqlquery": "SELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")", "query_result|header_prefix": "35", "query_result|header": "yes", "addqueries|queries_0|sqlquery": "SELECT * FROM psms WHERE confidence > 97.0", "addqueries|queries_0|query_result|header_prefix": "", "addqueries|queries_0|query_result|header": "yes"}, "job": {"model_class": "Job", "id": "98623284f686bc7c", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "state": "error", "exit_code": null, "create_time": "2024-09-03T06:59:45.209611", "update_time": "2024-09-03T06:59:49.873153", "galaxy_version": "24.1", "external_id": "gxy-mpbcg", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/137/configs/tmpljwbu6nc' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/137/configs/tmpmsqj69lx' -Q '/galaxy/server/database/jobs_directory/000/137/configs/tmpljwbu6nc' --comment_char='#' -o '/galaxy/server/database/objects/6/0/d/dataset_60da0121-d131-4f09-8906-54a9df5c81a7.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": [{\"__index__\": 0, \"query_result\": {\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}, \"sqlquery\": \"SELECT * FROM psms WHERE confidence > 97.0\"}]}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"SELECT scan,\\\"m/z\\\", \\\"Precursor m/z Error [ppm]\\\", Sequence, \\\"Protein(s)\\\", confidence FROM PSMs WHERE NOT re_search(', ',\\\"Protein(s)\\\")\"", "save_db": "false", "modify_database": "{\"sql_stmts\": [{\"__index__\": 0, \"sqlstmt\": \"UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0\"}]}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 9, \"columns\": \"1,3,2,6,14,19,23\", \"filter_type\": \"select_columns\"}}]}, \"table\": {\"values\": [{\"id\": 160, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"scan,,,,,,confidence\", \"column_names_from_first_line\": true, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"PSMs\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "f88cf8ee998749f2", "src": "hda", "uuid": "06d6bda3-00a4-44af-bf95-4105b34dca77"}}, "outputs": {"output": {"id": "4306367a50dd42eb", "src": "hda", "uuid": "60da0121-d131-4f09-8906-54a9df5c81a7"}, "output1": {"id": "287c916884dcddd5", "src": "hda", "uuid": "af560828-98a1-4e90-a79c-bb812ced1a2b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/0/6/d/dataset_06d6bda3-00a4-44af-bf95-4105b34dca77.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'scan,,,,,,confidence', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19, 23]}]}], 'sql_stmts': ['UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0'], 'queries': [{'query': 'SELECT * FROM psms WHERE confidence > 97.0', 'result_file': 'results0.tsv', 'header': ''}]}\n\nDB modification: UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0 \nrowcount: \n\nSQL: SELECT * FROM psms WHERE confidence > 97.0 \nrowcount: None\n\nSQL: \nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n \nrowcount: None\n", "job_stdout": null, "job_stderr": null, "stdout": "\nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n ", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/0/6/d/dataset_06d6bda3-00a4-44af-bf95-4105b34dca77.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'scan,,,,,,confidence', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19, 23]}]}], 'sql_stmts': ['UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0'], 'queries': [{'query': 'SELECT * FROM psms WHERE confidence > 97.0', 'result_file': 'results0.tsv', 'header': ''}]}\n\nDB modification: UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0 \nrowcount: \n\nSQL: SELECT * FROM psms WHERE confidence > 97.0 \nrowcount: None\n\nSQL: \nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n \nrowcount: None\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, exit_code: None, stderr: JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/0/6/d/dataset_06d6bda3-00a4-44af-bf95-4105b34dca77.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'scan,,,,,,confidence', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19, 23]}]}], 'sql_stmts': ['UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0'], 'queries': [{'query': 'SELECT * FROM psms WHERE confidence > 97.0', 'result_file': 'results0.tsv', 'header': ''}]}\n\nDB modification: UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0 \nrowcount: \n\nSQL: SELECT * FROM psms WHERE confidence > 97.0 \nrowcount: None\n\nSQL: \nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n \nrowcount: None\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, exit_code: None, stderr: JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/0/6/d/dataset_06d6bda3-00a4-44af-bf95-4105b34dca77.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'scan,,,,,,confidence', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19, 23]}]}], 'sql_stmts': ['UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0'], 'queries': [{'query': 'SELECT * FROM psms WHERE confidence > 97.0', 'result_file': 'results0.tsv', 'header': ''}]}\n\nDB modification: UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0 \nrowcount: \n\nSQL: SELECT * FROM psms WHERE confidence > 97.0 \nrowcount: None\n\nSQL: \nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n \nrowcount: None\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0, exit_code: None, stderr: JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/0/6/d/dataset_06d6bda3-00a4-44af-bf95-4105b34dca77.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'scan,,,,,,confidence', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19, 23]}]}], 'sql_stmts': ['UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0'], 'queries': [{'query': 'SELECT * FROM psms WHERE confidence > 97.0', 'result_file': 'results0.tsv', 'header': ''}]}\n\nDB modification: UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0 \nrowcount: \n\nSQL: SELECT * FROM psms WHERE confidence > 97.0 \nrowcount: None\n\nSQL: \nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n \nrowcount: None\n."], "status": "failure"}}, {"id": "query_tabular/3.3.0-9", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 9, "time_seconds": 31.527164220809937, "inputs": {"tables_0|table": {"src": "hda", "id": "ef2ef7ab93610131"}, "tables_0|input_opts|linefilters_0|filter|regex_pattern": "peptide", "tables_0|input_opts|linefilters_0|filter|regex_action": "include_find", "tables_0|input_opts|linefilters_0|filter|filter_type": "regex", "tables_0|tbl_opts|table_name": "epitope", "tables_0|tbl_opts|column_names_from_first_line": true, "sqlquery": "SELECT * FROM epitope", "query_result|header_prefix": "", "query_result|header": "yes"}, "job": {"model_class": "Job", "id": "4f537bd59150836b", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T07:00:08.783270", "update_time": "2024-09-03T07:00:21.520023", "galaxy_version": "24.1", "external_id": "gxy-9vs5k", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/139/configs/tmp2i9s9xas' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/139/configs/tmp_r877wgp' -Q '/galaxy/server/database/jobs_directory/000/139/configs/tmp2i9s9xas' -o '/galaxy/server/database/objects/4/3/6/dataset_436c83b1-570a-44d6-9780-e6bbc572a3d3.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}", "sqlquery": "\"SELECT * FROM epitope\"", "save_db": "false", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"peptide\"}}]}, \"table\": {\"values\": [{\"id\": 163, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"\", \"column_names_from_first_line\": true, \"indexes\": [], \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"table_name\": \"epitope\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "ef2ef7ab93610131", "src": "hda", "uuid": "17264408-078a-4185-b36d-8847c64e8338"}}, "outputs": {"output": {"id": "5a837dc38db3ef34", "src": "hda", "uuid": "436c83b1-570a-44d6-9780-e6bbc572a3d3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\nSELECT * FROM epitope\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/1/7/2/dataset_17264408-078a-4185-b36d-8847c64e8338.dat', 'table_name': 'epitope', 'firstlinenames': True, 'column_names': '', 'filters': [{'filter': 'regex', 'pattern': 'peptide', 'action': 'include_find'}]}]}\n\nSQL: \nSELECT * FROM epitope\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stdout": "\nSELECT * FROM epitope\n ", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/1/7/2/dataset_17264408-078a-4185-b36d-8847c64e8338.dat', 'table_name': 'epitope', 'firstlinenames': True, 'column_names': '', 'filters': [{'filter': 'regex', 'pattern': 'peptide', 'action': 'include_find'}]}]}\n\nSQL: \nSELECT * FROM epitope\n \nrowcount: None\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 07:00:10", "plugin": "core", "name": "end_epoch", "raw_value": "1725346810.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 07:00:10", "plugin": "core", "name": "start_epoch", "raw_value": "1725346810.0000000"}, {"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": "sam_pileup/1.1.3-0", "has_data": true, "data": {"tool_id": "sam_pileup", "tool_version": "1.1.3", "test_index": 0, "time_seconds": 34.649791955947876, "inputs": {"refOrHistory|input1": {"src": "hda", "id": "519c268d6e571334"}, "refOrHistory|ownFile": {"src": "hda", "id": "f9ab1f8db539c4c2"}, "refOrHistory|reference": "history", "lastCol": "no", "indels": "no", "mapCap": "60", "c|consensus": "no"}, "job": {"model_class": "Job", "id": "101b56dd69096d11", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3", "state": "error", "exit_code": 127, "create_time": "2024-09-03T06:52:31.325977", "update_time": "2024-09-03T06:52:46.150783", "galaxy_version": "24.1", "external_id": "gxy-kc4wx", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/0/6/5/dataset_06523432-b9d1-4891-b7d3-e4f400182d1f.dat' input1.bam && ln -s '/galaxy/server/database/objects/_metadata_files/8/5/3/metadata_853b3ca5-b2b1-4b83-8363-91890d787490.dat' 'input1.bam.bai' && ln -s '/galaxy/server/database/objects/3/b/b/dataset_3bb2da50-e1ca-44ce-a322-d63f5df29347.dat' reference.fasta && samtools faidx reference.fasta && samtools pileup -M 60 -f reference.fasta input1.bam > '/galaxy/server/database/objects/6/e/a/dataset_6eae9bca-de3a-49f3-a1fe-3848034e3fd9.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"equCab2\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/equCab2.len\"", "c": "{\"__current_case__\": 0, \"consensus\": \"no\"}", "mapCap": "\"60\"", "indels": "\"no\"", "lastCol": "\"no\"", "refOrHistory": "{\"__current_case__\": 1, \"input1\": {\"values\": [{\"id\": 127, \"src\": \"hda\"}]}, \"ownFile\": {\"values\": [{\"id\": 128, \"src\": \"hda\"}]}, \"reference\": \"history\"}"}, "inputs": {"refOrHistory|input1": {"id": "519c268d6e571334", "src": "hda", "uuid": "06523432-b9d1-4891-b7d3-e4f400182d1f"}, "refOrHistory|ownFile": {"id": "f9ab1f8db539c4c2", "src": "hda", "uuid": "3bb2da50-e1ca-44ce-a322-d63f5df29347"}}, "outputs": {"output1": {"id": "156ba8706e2576b1", "src": "hda", "uuid": "6eae9bca-de3a-49f3-a1fe-3848034e3fd9"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory\n", "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 127 ()", "error_level": 3, "exit_code": 127, "type": "exit_code"}], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:52:35", "plugin": "core", "name": "end_epoch", "raw_value": "1725346355.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:52:35", "plugin": "core", "name": "start_epoch", "raw_value": "1725346355.0000000"}, {"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"}]}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, exit_code: 127, stderr: samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.3, exit_code: 127, stderr: samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory\n."], "status": "failure"}}, {"id": "samtools_calmd/2.0.2-0", "has_data": true, "data": {"tool_id": "samtools_calmd", "tool_version": "2.0.2", "test_index": 0, "time_seconds": 37.68542551994324, "inputs": {"input_bam": {"src": "hda", "id": "60dc8ed2ca8581ac"}, "reference_source|ref_fasta": {"src": "hda", "id": "2446f7b193ccd43f"}, "reference_source|reference_source_selector": "history", "baq_settings|use_baq": "", "option_set|option_sets": "default"}, "job": {"model_class": "Job", "id": "e5bbc2df36210b85", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:53:08.277031", "update_time": "2024-09-03T06:53:24.438425", "galaxy_version": "24.1", "external_id": "gxy-xnc4c", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/5/c/5/dataset_5c5c06e5-29d0-49a7-b55c-fdfb5baadff9.dat' ref.fa && samtools faidx ref.fa && samtools calmd -b -@ $addthreads '/galaxy/server/database/objects/1/5/2/dataset_1526ed88-17bf-470b-8044-87a12f5dc1f4.dat' 'ref.fa' > '/galaxy/server/database/objects/a/1/f/dataset_a1fac533-fc32-4d7b-9232-92e21a19d0cc.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "option_set": "{\"__current_case__\": 0, \"option_sets\": \"default\"}", "baq_settings": "{\"__current_case__\": 0, \"extended_baq\": \"\", \"modify_quality\": \"\", \"use_baq\": \"\"}", "reference_source": "{\"__current_case__\": 1, \"ref_fasta\": {\"values\": [{\"id\": 131, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_bam": {"id": "60dc8ed2ca8581ac", "src": "hda", "uuid": "1526ed88-17bf-470b-8044-87a12f5dc1f4"}, "reference_source|ref_fasta": {"id": "2446f7b193ccd43f", "src": "hda", "uuid": "5c5c06e5-29d0-49a7-b55c-fdfb5baadff9"}}, "outputs": {"calmd_output": {"id": "16409116e0085a10", "src": "hda", "uuid": "a1fac533-fc32-4d7b-9232-92e21a19d0cc"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:53:13", "plugin": "core", "name": "end_epoch", "raw_value": "1725346393.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:53:13", "plugin": "core", "name": "start_epoch", "raw_value": "1725346393.0000000"}, {"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": "samtools_calmd/2.0.2-1", "has_data": true, "data": {"tool_id": "samtools_calmd", "tool_version": "2.0.2", "test_index": 1, "time_seconds": 32.51380181312561, "inputs": {"input_bam": {"src": "hda", "id": "312b94f173dc392f"}, "reference_source|ref_fasta": {"src": "hda", "id": "c70250f1936d4dbf"}, "reference_source|reference_source_selector": "history", "baq_settings|extended_baq": true, "baq_settings|use_baq": "-r", "option_set|change_identical": true, "option_set|adjust_mq": "50", "option_set|option_sets": "advanced"}, "job": {"model_class": "Job", "id": "3316eddaf4251de1", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:53:44.306425", "update_time": "2024-09-03T06:53:57.030427", "galaxy_version": "24.1", "external_id": "gxy-76826", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/b/a/0/dataset_ba0e9406-5672-47d8-9e02-7fb57f928309.dat' ref.fa && samtools faidx ref.fa && samtools calmd -r -E -e -C 50 -b -@ $addthreads '/galaxy/server/database/objects/5/b/d/dataset_5bd7e051-2ba9-48e1-9fd0-7542ac9bf44d.dat' 'ref.fa' > '/galaxy/server/database/objects/1/d/f/dataset_1dffe831-e25d-485a-8753-29acc8f63ce0.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "option_set": "{\"__current_case__\": 1, \"adjust_mq\": \"50\", \"change_identical\": true, \"option_sets\": \"advanced\"}", "baq_settings": "{\"__current_case__\": 1, \"extended_baq\": true, \"modify_quality\": false, \"use_baq\": \"-r\"}", "reference_source": "{\"__current_case__\": 1, \"ref_fasta\": {\"values\": [{\"id\": 134, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_bam": {"id": "312b94f173dc392f", "src": "hda", "uuid": "5bd7e051-2ba9-48e1-9fd0-7542ac9bf44d"}, "reference_source|ref_fasta": {"id": "c70250f1936d4dbf", "src": "hda", "uuid": "ba0e9406-5672-47d8-9e02-7fb57f928309"}}, "outputs": {"calmd_output": {"id": "db8ee8927138dbc6", "src": "hda", "uuid": "1dffe831-e25d-485a-8753-29acc8f63ce0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-03 06:53:47", "plugin": "core", "name": "end_epoch", "raw_value": "1725346427.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:53:46", "plugin": "core", "name": "start_epoch", "raw_value": "1725346426.0000000"}, {"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": "scanpy_parameter_iterator/0.0.1+galaxy0-0", "has_data": true, "data": {"tool_id": "scanpy_parameter_iterator", "tool_version": "0.0.1+galaxy0", "test_index": 0, "time_seconds": 34.47064280509949, "inputs": {"parameter_name": "perplexity", "input_type|input_values": "1, 5, 10", "input_type|parameter_values": "list_comma_separated_values"}, "job": {"model_class": "Job", "id": "4a45112de13adf14", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:55:03.353614", "update_time": "2024-09-03T06:55:37.182150", "galaxy_version": "24.1", "external_id": "gxy-n4cn7", "handler": null, "job_runner_name": null, "command_line": "mkdir outputs; for param in $(echo '1, 5, 10' | sed 's/,/ /g'); do echo $param > outputs/'perplexity'_$param\\.txt; done", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"data\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "input_type": "{\"__current_case__\": 0, \"input_values\": \"1, 5, 10\", \"parameter_values\": \"list_comma_separated_values\"}", "parameter_name": "\"perplexity\""}, "inputs": {}, "outputs": {"__new_primary_file_parameter_iteration|perplexity_1__": {"id": "0370dbf526dc9b2b", "src": "hda", "uuid": "aeb566d8-98d1-408b-a2a7-e31a199335e5"}, "__new_primary_file_parameter_iteration|perplexity_10__": {"id": "4f537bd59150836b", "src": "hda", "uuid": "acfdfb69-ce82-457e-b74b-c0d529ac6ecf"}, "__new_primary_file_parameter_iteration|perplexity_5__": {"id": "e2c84b674ab0a58a", "src": "hda", "uuid": "c4996610-b7a6-4e4e-b1e7-0e5b44a3d210"}}, "copied_from_job_id": null, "output_collections": {"parameter_iteration": {"src": "hdca", "id": "a80664568881873a"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 06:55:21", "plugin": "core", "name": "end_epoch", "raw_value": "1725346521.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 06:55:21", "plugin": "core", "name": "start_epoch", "raw_value": "1725346521.0000000"}, {"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"}]}, "output_problems": ["Collection element perplexity_1 of collection parameter_iteration: Test output file (perplexity_1.txt) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "scater_plot_exprs_freq/1.12.2-0", "has_data": true, "data": {"tool_id": "scater_plot_exprs_freq", "tool_version": "1.12.2", "test_index": 0, "time_seconds": 62.12353873252869, "inputs": {"input_loom": {"src": "hda", "id": "41280b56948002c0"}}, "job": {"model_class": "Job", "id": "d3313b4961f32071", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/scater_plot_exprs_freq/1.12.2", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T06:54:18.286095", "update_time": "2024-09-03T06:55:01.626221", "galaxy_version": "24.1", "external_id": "gxy-zltsp", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_exprs_freq/058b40656107/scater_plot_exprs_freq/scater-plot-exprs-freq.R' -i '/galaxy/server/database/objects/6/1/7/dataset_617c26fe-6b3d-4954-89e5-15a4a4f15548.dat' -o '/galaxy/server/database/objects/6/5/d/dataset_65dc56e6-ff07-411e-a868-68a8e43e3adf.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"loom\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input_loom": {"id": "41280b56948002c0", "src": "hda", "uuid": "617c26fe-6b3d-4954-89e5-15a4a4f15548"}}, "outputs": {"output_plot": {"id": "98623284f686bc7c", "src": "hda", "uuid": "65dc56e6-ff07-411e-a868-68a8e43e3adf"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Loading required package: S4Vectors\nLoading required package: stats4\nLoading required package: BiocGenerics\nLoading required package: parallel\n\nAttaching package: 'BiocGenerics'\n\nThe following objects are masked from 'package:parallel':\n\n clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n clusterExport, clusterMap, parApply, parCapply, parLapply,\n parLapplyLB, parRapply, parSapply, parSapplyLB\n\nThe following objects are masked from 'package:stats':\n\n IQR, mad, sd, var, xtabs\n\nThe following objects are masked from 'package:base':\n\n Filter, Find, Map, Position, Reduce, anyDuplicated, append,\n as.data.frame, basename, cbind, colnames, dirname, do.call,\n duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,\n lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,\n pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,\n tapply, union, unique, unsplit, which, which.max, which.min\n\n\nAttaching package: 'S4Vectors'\n\nThe following object is masked from 'package:base':\n\n expand.grid\n\nLoading required package: SingleCellExperiment\nLoading required package: SummarizedExperiment\nLoading required package: GenomicRanges\nLoading required package: IRanges\nLoading required package: GenomeInfoDb\nLoading required package: Biobase\nWelcome to Bioconductor\n\n Vignettes contain introductory material; view with\n 'browseVignettes()'. To cite Bioconductor, see\n 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\nLoading required package: DelayedArray\nLoading required package: matrixStats\n\nAttaching package: 'matrixStats'\n\nThe following objects are masked from 'package:Biobase':\n\n anyMissing, rowMedians\n\nLoading required package: BiocParallel\n\nAttaching package: 'DelayedArray'\n\nThe following objects are masked from 'package:matrixStats':\n\n colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges\n\nThe following objects are masked from 'package:base':\n\n aperm, apply, rowsum\n\nLoading required package: rhdf5\nLoading required package: rtracklayer\nLoading required package: ggplot2\n\nAttaching package: 'scater'\n\nThe following object is masked from 'package:S4Vectors':\n\n rename\n\nThe following object is masked from 'package:stats':\n\n filter\n\nSaving 7 x 7 in image\n`geom_smooth()` using method = 'loess' and formula 'y ~ x'\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Loading required package: S4Vectors\nLoading required package: stats4\nLoading required package: BiocGenerics\nLoading required package: parallel\n\nAttaching package: 'BiocGenerics'\n\nThe following objects are masked from 'package:parallel':\n\n clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n clusterExport, clusterMap, parApply, parCapply, parLapply,\n parLapplyLB, parRapply, parSapply, parSapplyLB\n\nThe following objects are masked from 'package:stats':\n\n IQR, mad, sd, var, xtabs\n\nThe following objects are masked from 'package:base':\n\n Filter, Find, Map, Position, Reduce, anyDuplicated, append,\n as.data.frame, basename, cbind, colnames, dirname, do.call,\n duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,\n lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,\n pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,\n tapply, union, unique, unsplit, which, which.max, which.min\n\n\nAttaching package: 'S4Vectors'\n\nThe following object is masked from 'package:base':\n\n expand.grid\n\nLoading required package: SingleCellExperiment\nLoading required package: SummarizedExperiment\nLoading required package: GenomicRanges\nLoading required package: IRanges\nLoading required package: GenomeInfoDb\nLoading required package: Biobase\nWelcome to Bioconductor\n\n Vignettes contain introductory material; view with\n 'browseVignettes()'. To cite Bioconductor, see\n 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\nLoading required package: DelayedArray\nLoading required package: matrixStats\n\nAttaching package: 'matrixStats'\n\nThe following objects are masked from 'package:Biobase':\n\n anyMissing, rowMedians\n\nLoading required package: BiocParallel\n\nAttaching package: 'DelayedArray'\n\nThe following objects are masked from 'package:matrixStats':\n\n colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges\n\nThe following objects are masked from 'package:base':\n\n aperm, apply, rowsum\n\nLoading required package: rhdf5\nLoading required package: rtracklayer\nLoading required package: ggplot2\n\nAttaching package: 'scater'\n\nThe following object is masked from 'package:S4Vectors':\n\n rename\n\nThe following object is masked from 'package:stats':\n\n filter\n\nSaving 7 x 7 in image\n`geom_smooth()` using method = 'loess' and formula 'y ~ x'\n", "job_messages": [], "dependencies": [], 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{"model_class": "Job", "id": "00e9c169862726a9", "history_id": "c5fe43971bba42f1", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-03T07:04:21.613439", "update_time": "2024-09-03T07:04:39.464305", "galaxy_version": "24.1", "external_id": "gxy-ptvnf", "handler": null, "job_runner_name": null, "command_line": "vcfcommonsamples '/galaxy/server/database/objects/1/0/4/dataset_104dbe11-503a-49b5-ab60-b2bcf328fdaf.dat' '/galaxy/server/database/objects/2/a/a/dataset_2aaee688-aad9-4401-b8f5-54a8cca3d4e0.dat' > '/galaxy/server/database/objects/7/e/2/dataset_7e2f22b7-bfbf-47ec-a19c-c188d884f442.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input1": {"id": "86a823b605317ef5", "src": "hda", "uuid": 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'/galaxy/server/database/objects/f/a/a/dataset_faaf6962-d720-4a28-9440-955709a9f7cd.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input1": {"id": "ff54342be9566e67", "src": "hda", "uuid": "cd94dda2-9ce9-4bae-8d7a-f3284c5d6167"}}, "outputs": {"out_file1": {"id": "09220a8ae80fea8d", "src": "hda", "uuid": "faaf6962-d720-4a28-9440-955709a9f7cd"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-03 07:05:00", "plugin": "core", "name": "end_epoch", "raw_value": "1725347100.0000000"}, {"title": "Job Start Time", "value": "2024-09-03 07:05:00", "plugin": "core", "name": "start_epoch", "raw_value": "1725347100.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}], "galaxy_url": "http://34.75.106.159:8000/galaxy/"} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/results.xunit b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/results.xunit new file mode 100644 index 000000000..c48395bcc --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/results.xunit @@ -0,0 +1,880 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + sys.exit(main()) ^^^^^^ File "/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py", line 99, in main Groomer().run() File "/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py", line 48, in run for read_count, fastq_read in enumerate(reader): File "/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py", line 683, in __iter__ yield next(self) ^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py", line 742, in __next__ raise e File "/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py", line 724, in __next__ block = super(fastqVerboseErrorReader, self).__next__() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py", line 621, in __next__ self._read_fastq_sequence(rval, id_line) File "/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py", line 666, in _read_fastq_sequence raise fastqFormatError(galaxy_utils.sequence.fastq.fastqFormatError: Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1). + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Step 1: reading read mappings <===[M::ma_hit_read::0.150*1.00] read 100000 hits; stored 187742 hits and 12067 sequences (111354001 bp)[M::main] ===> Step 2: 1-pass (crude) read selection <===[M::ma_hit_sub::0.170*1.00] 9155 query sequences remain after sub[M::ma_hit_cut::0.175*1.00] 161122 hits remain after cut[M::ma_hit_flt::0.177*1.00] 156936 hits remain after filtering; crude coverage after filtering: 11.85[M::main] ===> Step 3: 2-pass (fine) read selection <===[M::ma_hit_sub::0.187*1.00] 9023 query sequences remain after sub[M::ma_hit_cut::0.188*1.00] 152071 hits remain after cut[M::ma_hit_contained::0.192*1.00] 1536 sequences and 8359 hits remain after containment removal[M::main] ===> Step 4: graph cleaning <===[M::ma_sg_gen] read 8236 arcs[M::main] ===> Step 4.1: transitive reduction <===[M::asg_arc_del_trans] transitively reduced 4182 arcs[M::asg_arc_del_multi] removed 0 multi-arcs[M::asg_arc_del_asymm] removed 362 asymmetric arcs[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===[M::asg_cut_tip] cut 260 tips[M::asg_pop_bubble] popped 105 bubbles and trimmed 4 tips[M::main] ===> Step 4.3: cutting short overlaps (3 rounds in total) <===[M::asg_arc_del_multi] removed 0 multi-arcs[M::asg_arc_del_asymm] removed 29 asymmetric arcs[M::asg_arc_del_short] removed 37 short overlaps[M::asg_cut_tip] cut 104 tips[M::asg_pop_bubble] popped 1 bubbles and trimmed 0 tips[M::asg_arc_del_multi] removed 0 multi-arcs[M::asg_arc_del_asymm] removed 1 asymmetric arcs[M::asg_arc_del_short] removed 1 short overlaps[M::asg_cut_tip] cut 3 tips[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips[M::asg_arc_del_short] removed 0 short overlaps[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===[M::asg_cut_internal] cut 0 internal sequences[M::asg_cut_biloop] cut 0 small bi-loops[M::asg_cut_tip] cut 0 tips[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips[M::main] ===> Step 4.5: aggressively cutting short overlaps <===[M::asg_arc_del_short] removed 0 short overlaps[M::main] ===> Step 5: generating unitigs <===[M::main] Version: 0.3-r179[M::main] CMD: miniasm -f /galaxy/server/database/objects/0/b/a/dataset_0ba5d077-2fd3-4d97-8b5b-a34154168183.dat -m 100 -i 0.05 -s 1000 -c 3 -o 1000 -h 1000 -I 0.08 -g 1000 -d 50000 -e 4 -n 3 -F 0.8 /galaxy/server/database/objects/9/5/d/dataset_95da33ab-f618-4e90-9816-59b7efabc33c.dat[M::main] Real time: 0.203 sec; CPU: 0.201 sec + ]]> + + + + + + + + Step 1: reading read mappings <===[M::ma_hit_read::0.151*1.00] read 100000 hits; stored 187766 hits and 12068 sequences (111355211 bp)[M::main] ===> Step 2: 1-pass (crude) read selection <===[M::ma_hit_sub::0.171*1.00] 10122 query sequences remain after sub[M::ma_hit_cut::0.173*1.00] 171862 hits remain after cut[M::ma_hit_flt::0.175*1.00] 165533 hits remain after filtering; crude coverage after filtering: 11.51[M::main] ===> Step 3: 2-pass (fine) read selection <===[M::ma_hit_sub::0.186*1.00] 9994 query sequences remain after sub[M::ma_hit_cut::0.188*1.00] 163595 hits remain after cut[M::ma_hit_contained::0.192*1.00] 1772 sequences and 10061 hits remain after containment removal[M::main] ===> Step 4: graph cleaning <===[M::ma_sg_gen] read 9758 arcs[M::main] ===> Step 4.1: transitive reduction <===[M::asg_arc_del_trans] transitively reduced 4694 arcs[M::asg_arc_del_multi] removed 0 multi-arcs[M::asg_arc_del_asymm] removed 484 asymmetric arcs[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===[M::asg_cut_tip] cut 282 tips[M::asg_pop_bubble] popped 173 bubbles and trimmed 6 tips[M::main] ===> Step 4.3: cutting short overlaps (2 rounds in total) <===[M::asg_arc_del_multi] removed 0 multi-arcs[M::asg_arc_del_asymm] removed 26 asymmetric arcs[M::asg_arc_del_short] removed 38 short overlaps[M::asg_cut_tip] cut 53 tips[M::asg_pop_bubble] popped 8 bubbles and trimmed 0 tips[M::asg_arc_del_multi] removed 0 multi-arcs[M::asg_arc_del_asymm] removed 2 asymmetric arcs[M::asg_arc_del_short] removed 2 short overlaps[M::asg_cut_tip] cut 2 tips[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===[M::asg_cut_internal] cut 0 internal sequences[M::asg_cut_biloop] cut 0 small bi-loops[M::asg_cut_tip] cut 0 tips[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips[M::main] ===> Step 4.5: aggressively cutting short overlaps <===[M::asg_arc_del_short] removed 0 short overlaps[M::main] ===> Step 5: generating unitigs <===[M::main] Version: 0.3-r179[M::main] CMD: miniasm -f /galaxy/server/database/objects/9/7/b/dataset_97b02566-59f7-453e-b759-3f75fa0eab19.dat -m 99 -i 0.04 -s 999 -c 2 -o 999 -h 999 -I 0.7 -g 999 -d 45000 -e 3 -n 2 -F 0.7 /galaxy/server/database/objects/4/4/5/dataset_445026e0-dc80-4d1c-95a7-ef2a720e4cfe.dat[M::main] Real time: 0.206 sec; CPU: 0.205 sec + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 97.0', 'result_file': 'results0.tsv', 'header': ''}]}DB modification: UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0 rowcount: SQL: SELECT * FROM psms WHERE confidence > 97.0 rowcount: NoneSQL: SELECT scan,"m/z", "Precursor m/z Error [ppm]", Sequence, "Protein(s)", confidence FROM PSMs WHERE NOT re_search(', ',"Protein(s)") rowcount: None + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/tools.yml b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/tools.yml new file mode 100644 index 000000000..08a6e2b7b --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-03-06-11-1/tools.yml @@ -0,0 +1,122 @@ +chunk: 2 +tools: +- name: miniasm + owner: iuc + revisions: + - 8dee0218ac7d + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: deeptools_bigwig_compare + owner: bgruening + revisions: + - 26e7304d6737 + tool_panel_section_id: deeptools + tool_panel_section_label: deepTools +- name: fastq_groomer + owner: devteam + revisions: + - 47e5dbc3e790 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: sra_tools + owner: iuc + revisions: + - 83c7d564b128 + tool_panel_section_id: get_data + tool_panel_section_label: Get Data +- name: mummer_mummerplot + owner: iuc + revisions: + - ebe3b0f84de9 + tool_panel_section_id: multiple_alignments + tool_panel_section_label: Multiple Alignments +- name: poretools_qualpos + owner: iuc + revisions: + - 4fe6b96aff72 + tool_panel_section_id: nanopore + tool_panel_section_label: Nanopore +- name: kallisto_pseudo + owner: iuc + revisions: + - 5ae5c312d718 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: sam_pileup + owner: devteam + revisions: + - a3b4ad6858ff + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: samtools_calmd + owner: devteam + revisions: + - 06dc50b7b711 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: music_manipulate_eset + owner: bgruening + revisions: + - 22232092be53 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: droplet_barcode_plot + owner: ebi-gxa + revisions: + - 8f605643ccfd + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scater_plot_exprs_freq + owner: iuc + revisions: + - 058b40656107 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_parameter_iterator + owner: ebi-gxa + revisions: + - 0387a2179f88 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: query_tabular + owner: iuc + revisions: + - cf34c344508d + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: column_remove_by_header + owner: iuc + revisions: + - 372967836e98 + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: snpsift + owner: iuc + revisions: + - 2e497a770bca + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: bcftools_plugin_mendelian + owner: iuc + revisions: + - bf235558f2cf + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: bcftools_csq + owner: iuc + revisions: + - fdd127bd4a32 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: vcfcommonsamples + owner: devteam + revisions: + - f1852ecef841 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: vcfdistance + owner: iuc + revisions: + - c506b8275b1a + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF