From 8da10c1f0120cd9371846d867ba239dcaff0d42d Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Sat, 14 Sep 2024 01:17:57 +0000 Subject: [PATCH] Updating anvil-production README for prod-24-09-14-00-32-1 --- reports/anvil-production/README.md | 2 +- .../anvil-production/tool-tests/chunks.json | 10 +- .../prod-24-09-14-00-32-1/chunk.json | 7 + .../prod-24-09-14-00-32-1/chunk.txt | 15 + .../errors/0aec0cc69095fb2b.json | 44 + .../errors/219eea5edfdc4ae8.json | 44 + .../errors/4b3b265db2b6345e.json | 44 + .../errors/4f3352db0d5bc390.json | 49 + .../errors/64262c26ef4b4f8c.json | 44 + .../errors/877faa65ca7adf3a.json | 44 + .../errors/a6000a46566a855e.json | 44 + .../errors/da2d40552de3029b.json | 51 + .../errors/f513f03dee6ba111.json | 56 + .../errors/fe0a9ea15b54bf6c.json | 44 + .../prod-24-09-14-00-32-1/job-metrics.csv | 129 + .../tool-tests/prod-24-09-14-00-32-1/job.log | 4029 +++++++++++++++++ .../tool-tests/prod-24-09-14-00-32-1/jobs.txt | 128 + .../prod-24-09-14-00-32-1/node-info.txt | 146 + .../prod-24-09-14-00-32-1/results.html | 291 ++ .../prod-24-09-14-00-32-1/results.json | 1 + .../prod-24-09-14-00-32-1/results.xunit | 704 +++ .../prod-24-09-14-00-32-1/tools.yml | 92 + 22 files changed, 6012 insertions(+), 6 deletions(-) create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/chunk.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/chunk.txt create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/0aec0cc69095fb2b.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/219eea5edfdc4ae8.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/4b3b265db2b6345e.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/4f3352db0d5bc390.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/64262c26ef4b4f8c.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/877faa65ca7adf3a.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/a6000a46566a855e.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/da2d40552de3029b.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/f513f03dee6ba111.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/fe0a9ea15b54bf6c.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/job-metrics.csv create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/job.log create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/jobs.txt create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/node-info.txt create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/results.html create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/results.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/results.xunit create mode 100644 reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/tools.yml diff --git a/reports/anvil-production/README.md b/reports/anvil-production/README.md index e946bf311..abdbb74cf 100644 --- a/reports/anvil-production/README.md +++ b/reports/anvil-production/README.md @@ -13,4 +13,4 @@ After each successful deployment, automated tool tests are also run against the Latest tool tests for each chunk: -
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 09 00:49:24 2024Mon Sep 02 00:49:36 2024
1ToolsetMon Sep 09 12:50:13 2024Mon Sep 02 12:49:25 2024
2ToolsetTue Sep 10 00:48:20 2024Tue Sep 03 00:47:25 2024
3ToolsetTue Sep 10 12:51:55 2024Tue Sep 03 12:49:09 2024
4ToolsetWed Sep 04 00:47:35 2024Wed Aug 28 00:47:17 2024
5ToolsetWed Sep 11 12:50:17 2024Wed Sep 04 12:49:18 2024
6ToolsetThu Sep 12 00:49:13 2024Thu Sep 05 00:47:53 2024
7ToolsetThu Sep 12 12:49:05 2024Thu Aug 29 12:48:26 2024
8ToolsetFri Sep 13 00:47:48 2024Fri Sep 06 00:47:43 2024
9ToolsetFri Sep 13 12:48:35 2024Fri Sep 06 12:48:21 2024
10ToolsetSat Sep 07 00:54:23 2024Sat Aug 31 00:46:38 2024
11ToolsetSat Sep 07 12:45:43 2024Sat Aug 31 12:46:14 2024
12ToolsetSun Sep 08 00:51:47 2024Sun Sep 01 00:54:13 2024
13ToolsetSun Sep 08 12:46:16 2024Sun Sep 01 12:46:15 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 09 00:49:24 2024Mon Sep 02 00:49:36 2024
1ToolsetMon Sep 09 12:50:13 2024Mon Sep 02 12:49:25 2024
2ToolsetTue Sep 10 00:48:20 2024Tue Sep 03 00:47:25 2024
3ToolsetTue Sep 10 12:51:55 2024Tue Sep 03 12:49:09 2024
4ToolsetWed Sep 04 00:47:35 2024Wed Aug 28 00:47:17 2024
5ToolsetWed Sep 11 12:50:17 2024Wed Sep 04 12:49:18 2024
6ToolsetThu Sep 12 00:49:13 2024Thu Sep 05 00:47:53 2024
7ToolsetThu Sep 12 12:49:05 2024Thu Aug 29 12:48:26 2024
8ToolsetFri Sep 13 00:47:48 2024Fri Sep 06 00:47:43 2024
9ToolsetFri Sep 13 12:48:35 2024Fri Sep 06 12:48:21 2024
10ToolsetSat Sep 14 00:47:35 2024Sat Sep 07 00:54:23 2024
11ToolsetSat Sep 07 12:45:43 2024Sat Aug 31 12:46:14 2024
12ToolsetSun Sep 08 00:51:47 2024Sun Sep 01 00:54:13 2024
13ToolsetSun Sep 08 12:46:16 2024Sun Sep 01 12:46:15 2024
diff --git a/reports/anvil-production/tool-tests/chunks.json b/reports/anvil-production/tool-tests/chunks.json index 996d210f4..4c8e54256 100644 --- a/reports/anvil-production/tool-tests/chunks.json +++ b/reports/anvil-production/tool-tests/chunks.json @@ -7,11 +7,11 @@ "date2": "Thu Sep 05 00:47:53 2024" }, "10": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-07-00-31-1/results.html", - "date1": "Sat Sep 07 00:54:23 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-07-00-31-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-31-00-32-1/results.html", - "date2": "Sat Aug 31 00:46:38 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/results.html", + "date1": "Sat Sep 14 00:47:35 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-07-00-31-1/results.html", + "date2": "Sat Sep 07 00:54:23 2024" }, "11": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-07-12-30-1/results.html", diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/chunk.json b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/chunk.json new file mode 100644 index 000000000..c3da627bd --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/chunk.json @@ -0,0 +1,7 @@ +{ + "10": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/results.html", + "date1": "Sat Sep 14 00:47:35 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/chunk.txt b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/chunk.txt new file mode 100644 index 000000000..8b52783d8 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/chunk.txt @@ -0,0 +1,15 @@ +-t annotatemyids --tool-version 44018dd6b447 +-t datamash_reverse --tool-version 0f1724dd59d2 +-t trimmomatic --tool-version d94aff5ee623 +-t samtools_fixmate --tool-version bc0cc7bfbfe9 +-t sam_to_bam --tool-version cf1ffd88f895 +-t bcftools_plugin_setgt --tool-version 8abfcd1a6949 +-t bcftools_call --tool-version 072f606e2e69 +-t vcfbreakcreatemulti --tool-version 9fd5d91eb91b +-t vcfselectsamples --tool-version 2ba3b87f904f +-t poretools_occupancy --tool-version 338d15b8d6fb +-t deeptools_plot_heatmap --tool-version a4dfb122e52b +-t deeptools_plot_profile --tool-version c361b12d207a +-t lofreq_filter --tool-version 7dfca164d2e3 +-t salmon --tool-version cc05793bb896 +-t mummer_mummerplot --tool-version ebe3b0f84de9 diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/0aec0cc69095fb2b.json b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/0aec0cc69095fb2b.json new file mode 100644 index 000000000..47b487adb --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/0aec0cc69095fb2b.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "0aec0cc69095fb2b", + "state": "error", + "exit_code": null, + "update_time": 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b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/219eea5edfdc4ae8.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "219eea5edfdc4ae8", + "state": "error", + "exit_code": null, + "update_time": "2024-09-14T01:00:45.403522", + "create_time": "2024-09-14T01:00:35.519784", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "ed165837e8ba4cca", + "external_id": "gxy-xpxbv", + "command_line": "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' '72:/galaxy/server/database/objects/c/d/3/dataset_cd37bd50-8ef0-44f6-9550-06b20e271e97_files:/galaxy/server/database/objects/c/d/3/dataset_cd37bd50-8ef0-44f6-9550-06b20e271e97.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_f8gboh6h\"", + 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a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/4b3b265db2b6345e.json b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/4b3b265db2b6345e.json new file mode 100644 index 000000000..87e83e9b1 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/4b3b265db2b6345e.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "4b3b265db2b6345e", + "state": "error", + "exit_code": null, + "update_time": "2024-09-14T01:03:51.267360", + "create_time": "2024-09-14T01:03:42.535494", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "ed165837e8ba4cca", + "external_id": "gxy-pqs99", + "command_line": "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' 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'/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' '42:/galaxy/server/database/objects/6/c/4/dataset_6c491894-0ad3-4510-a9c4-8a10c6045ac5_files:/galaxy/server/database/objects/6/c/4/dataset_6c491894-0ad3-4510-a9c4-8a10c6045ac5.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_v9lz7191\"", + "files_metadata": "{\"__current_case__\": 82, \"file_type\": \"fastqsanger.gz\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"Illumina_SG_R2.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_g7mkis2m\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "3b076214a691ebd7", + "src": "hda", + "uuid": "6c491894-0ad3-4510-a9c4-8a10c6045ac5" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/877faa65ca7adf3a.json b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/877faa65ca7adf3a.json new file mode 100644 index 000000000..c98da0ac4 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/877faa65ca7adf3a.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "877faa65ca7adf3a", + "state": "error", + "exit_code": null, + "update_time": "2024-09-14T00:55:45.136973", + "create_time": "2024-09-14T00:55:35.975247", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "ed165837e8ba4cca", + "external_id": "gxy-ww4c7", + "command_line": "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' '40:/galaxy/server/database/objects/d/3/9/dataset_d393355a-1c2b-44f2-8534-fa14c8a5a6c0_files:/galaxy/server/database/objects/d/3/9/dataset_d393355a-1c2b-44f2-8534-fa14c8a5a6c0.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_e2o2iltb\"", + "files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"Illumina_SG_R2.fastq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_nt66jhoa\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "873462c21322a5f4", + "src": "hda", + "uuid": "d393355a-1c2b-44f2-8534-fa14c8a5a6c0" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/a6000a46566a855e.json b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/a6000a46566a855e.json new file mode 100644 index 000000000..dc9e0da27 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/a6000a46566a855e.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "a6000a46566a855e", + "state": "error", + "exit_code": null, + "update_time": "2024-09-14T00:55:09.420570", + "create_time": "2024-09-14T00:55:01.221058", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "ed165837e8ba4cca", + "external_id": "gxy-sf4nz", + "command_line": "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' '35:/galaxy/server/database/objects/b/c/d/dataset_bcda9236-4541-4155-8ce6-4c842913f7b4_files:/galaxy/server/database/objects/b/c/d/dataset_bcda9236-4541-4155-8ce6-4c842913f7b4.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_z3iggls3\"", + "files_metadata": "{\"__current_case__\": 84, \"file_type\": \"fastqsolexa\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"Illumina_SG_R1.fastqsolexa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_0z6w7l2r\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsolexa\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "14174cb4b325ed48", + "src": "hda", + "uuid": "bcda9236-4541-4155-8ce6-4c842913f7b4" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/da2d40552de3029b.json b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/da2d40552de3029b.json new file mode 100644 index 000000000..577fb57e5 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/da2d40552de3029b.json @@ -0,0 +1,51 @@ +{ + "model_class": "Job", + "id": "da2d40552de3029b", + "state": "error", + "exit_code": null, + "update_time": "2024-09-14T00:56:52.038033", + "create_time": "2024-09-14T00:56:47.840310", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1", + "history_id": "ed165837e8ba4cca", + "external_id": "gxy-q74tk", + "command_line": "if [ -z \"$TRIMMOMATIC_JAR_PATH\" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z \"$TRIMMOMATIC_ADAPTERS_PATH\" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/3/7/7/dataset_37778b71-9669-4df5-880b-532f8c4b276b.dat' fastq_in.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger' fastq_out.'fastqsanger' MAXINFO:75:0.8 2>&1 | tee trimmomatic.log && if [ -z \"$(tail -1 trimmomatic.log | grep \"Completed successfully\")\" ]; then echo \"Trimmomatic did not finish successfully\" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger' '/galaxy/server/database/objects/e/6/a/dataset_e6ac6186-9f77-45ca-a14f-43c8894a7811.dat'", + "traceback": null, + "params": { + "__input_ext": "\"fastqsanger\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "output_err": "false", + "output_logs": "false", + "operations": "[{\"__index__\": 0, \"operation\": {\"__current_case__\": 7, \"name\": \"MAXINFO\", \"strictness\": \"0.8\", \"target_length\": \"75\"}}]", + "illuminaclip": "{\"__current_case__\": 1, \"do_illuminaclip\": false}", + "readtype": "{\"__current_case__\": 0, \"fastq_in\": {\"values\": [{\"id\": 45, \"src\": \"hda\"}]}, \"single_or_paired\": \"se\"}" + }, + "inputs": { + "readtype|fastq_in": { + "id": "346ee1d2fcf7f70c", + "src": "hda", + "uuid": "37778b71-9669-4df5-880b-532f8c4b276b" + } + }, + "outputs": { + "fastq_out": { + "id": "50872bd7722d341d", + "src": "hda", + "uuid": "e6ac6186-9f77-45ca-a14f-43c8894a7811" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/f513f03dee6ba111.json b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/f513f03dee6ba111.json new file mode 100644 index 000000000..a24ddc5c6 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/f513f03dee6ba111.json @@ -0,0 +1,56 @@ +{ + "model_class": "Job", + "id": "f513f03dee6ba111", + "state": "error", + "exit_code": null, + "update_time": "2024-09-14T01:06:36.828805", + "create_time": "2024-09-14T01:06:31.054100", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", + "history_id": "ed165837e8ba4cca", + "external_id": "gxy-tbxfz", + "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/b/8/5/dataset_b851b4ac-86be-4622-bbe1-cc1c4d60f388.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --targets-file \"/galaxy/server/database/objects/f/9/a/dataset_f9ab92a9-992d-4798-8921-d967a0352f8b.dat\" --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/a/1/a/dataset_a1aa4eef-f0a9-4302-bc82-9e4cd2d6448a.dat'", + "traceback": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "output_type": "\"v\"", + "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": false, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": null, \"skip_variants\": null, \"variants_only\": false}", + "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", + "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 0, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\", \"targets\": {\"__current_case__\": 2, \"invert_targets_file\": false, \"targets_file\": {\"values\": [{\"id\": 104, \"src\": \"hda\"}]}, \"targets_src\": \"targets_file\"}, \"targets_overlap\": null}, \"gvcf\": \"\", \"method\": \"multiallelic\", \"prior\": \"0.0011\", \"prior_freqs\": \"\"}}", + "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}" + }, + "inputs": { + "input_file": { + "id": "4f3352db0d5bc390", + "src": "hda", + "uuid": "b851b4ac-86be-4622-bbe1-cc1c4d60f388" + }, + "sec_consensus_variant_calling|variant_calling|genotypes|targets|targets_file": { + "id": "cbd23c4cd10aa88a", + "src": "hda", + "uuid": "f9ab92a9-992d-4798-8921-d967a0352f8b" + } + }, + "outputs": { + "output_file": { + "id": "fb28fb836c18096d", + "src": "hda", + "uuid": "a1aa4eef-f0a9-4302-bc82-9e4cd2d6448a" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/fe0a9ea15b54bf6c.json b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/fe0a9ea15b54bf6c.json new file mode 100644 index 000000000..82d204c85 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/errors/fe0a9ea15b54bf6c.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "fe0a9ea15b54bf6c", + "state": "error", + "exit_code": null, + "update_time": "2024-09-14T00:53:23.031439", + "create_time": "2024-09-14T00:53:14.186609", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "ed165837e8ba4cca", + "external_id": "gxy-rzcrg", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/13/registry.xml' '/galaxy/server/database/jobs_directory/000/13/upload_params.json' '16:/galaxy/server/database/objects/d/d/7/dataset_dd7cfbb0-f7a0-489a-868d-01808f00a8fd_files:/galaxy/server/database/objects/d/d/7/dataset_dd7cfbb0-f7a0-489a-868d-01808f00a8fd.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_8pius79c\"", + "files_metadata": "{\"__current_case__\": 82, \"file_type\": \"fastqsanger.gz\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"Illumina_SG_R1.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ut5pdeks\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger.gz\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "7bf7e48be40dc04d", + "src": "hda", + "uuid": "dd7cfbb0-f7a0-489a-868d-01808f00a8fd" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/job-metrics.csv b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/job-metrics.csv new file mode 100644 index 000000000..5c86eaf6f --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/job-metrics.csv @@ -0,0 +1,129 @@ +id,history_id,history_name,state,tool_id,invocation_id,workflow_id,cpuacct.usage,galaxy_memory_mb,galaxy_slots,memory.limit_in_bytes,memory.peak,memory.soft_limit_in_bytes,memtotal,processor_count,runtime_seconds +b7c0a16325039497,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,mummer_mummerplot/4.0.0rc1+galaxy3,,,,4080.0000000,1.0000000,,,,,,0E-7 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+22470166765b2f95,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,lofreq_filter/2.1.5+galaxy0,,,,16320.0000000,1.0000000,,,,,,1.0000000 +251b4eb87d395ff4,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +ffe3188988274058,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,lofreq_filter/2.1.5+galaxy0,,,,16320.0000000,1.0000000,,,,,,0E-7 +2ca487e824fa2a6a,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +4c4c4e06aa36dd6f,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,lofreq_filter/2.1.5+galaxy0,,,,16320.0000000,1.0000000,,,,,,0E-7 +6866e8eee2e30678,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +fb28fb836c18096d,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,deeptools_plot_profile/3.5.4+galaxy0,,,,21474.0000000,1.0000000,,,,,,3.0000000 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+022a03c7fd9fc863,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,poretools_occupancy/0.6.1a1.1,,,,12240.0000000,1.0000000,,,,,,3.0000000 +b914c5cbdc32f1b4,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +50976ab105970f33,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,poretools_occupancy/0.6.1a1.1,,,,12240.0000000,1.0000000,,,,,,3.0000000 +153dc00d25d9a6d7,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +fb8ab536889f0e94,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,vcfselectsamples/1.0.0_rc3+galaxy0,,,,4080.0000000,1.0000000,,,,,,0E-7 +748366871c7f2141,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +d58abde2fb36f1e8,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,vcfbreakcreatemulti/1.0.0_rc3+galaxy0,,,,4080.0000000,1.0000000,,,,,,0E-7 +c9147cfbb24d024f,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +e5e85752534a1f6b,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,vcfbreakcreatemulti/1.0.0_rc3+galaxy0,,,,4080.0000000,1.0000000,,,,,,0E-7 +6872c13e0305d080,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +f513f03dee6ba111,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,error,bcftools_call/1.15.1+galaxy5,,,,,,,,,,, +1747158b9458f9f7,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +0ac6b3678845426c,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +16a1aab48891616f,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,bcftools_call/1.15.1+galaxy5,,,,4080.0000000,1.0000000,,,,,,0E-7 +1913c0b28f54e065,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +050fdb9488518af8,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,bcftools_call/1.15.1+galaxy5,,,,4080.0000000,1.0000000,,,,,,1.0000000 +5c0d3387021faa81,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +0dd086a5fc3869bf,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,bcftools_call/1.15.1+galaxy5,,,,4080.0000000,1.0000000,,,,,,1.0000000 +6392c2499aa3e408,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +d49c36adeba8557f,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +b94e2d0d46c75809,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,bcftools_call/1.15.1+galaxy5,,,,4080.0000000,1.0000000,,,,,,1.0000000 +b355a78f591d3088,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +dc1abf31b7878b39,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +2611c7230f4ebe6d,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,bcftools_call/1.15.1+galaxy5,,,,4080.0000000,1.0000000,,,,,,1.0000000 +c12cff306b1f27cd,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +2c20b2126db3a04f,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +fa93e67c1e1ebcf1,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +4b3b265db2b6345e,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,error,upload1,,,,,,,,,,, +87dadb2c71819a0b,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,bcftools_call/1.15.1+galaxy5,,,,4080.0000000,1.0000000,,,,,,1.0000000 +ab33a4ba552f72dc,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +1a9d1a58818c88c1,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,bcftools_plugin_setgt/1.15.1+galaxy4,,,,4080.0000000,1.0000000,,,,,,1.0000000 +548270c1cda12d7a,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +5138b028115a7f5f,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,bcftools_plugin_setgt/1.15.1+galaxy4,,,,4080.0000000,1.0000000,,,,,,1.0000000 +6ec8bf3c5dc3224e,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +24e58a97d82a5b14,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,sam_to_bam/2.1.2,,,,4080.0000000,1.0000000,,,,,,0E-7 +54816788543a0d5a,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +1e7e26c0720680d3,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +1762d3613701af86,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,sam_to_bam/2.1.2,,,,4080.0000000,1.0000000,,,,,,0E-7 +9cbc3100f8d963dc,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +58bcb7304f57378f,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +95a0a0882149fa40,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,sam_to_bam/2.1.2,,,,4080.0000000,1.0000000,,,,,,0E-7 +5df7adb272208d2d,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +2ea84bc3d4af7b79,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +219eea5edfdc4ae8,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,error,upload1,,,,,,,,,,, +0aec0cc69095fb2b,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,error,upload1,,,,,,,,,,, +4fe3ac1409aa61b5,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,samtools_fixmate/1.9,,,,4080.0000000,1.0000000,,,,,,0E-7 +d0d1c4024af98dfb,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +517cff8f48d5d3c0,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,samtools_fixmate/1.9,,,,4080.0000000,1.0000000,,,,,,0E-7 +9184366d0e5e1098,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +169d16a8c5164f68,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,samtools_fixmate/1.9,,,,4080.0000000,1.0000000,,,,,,0E-7 +9907fa81e6c94704,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +50872bd7722d341d,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,samtools_fixmate/1.9,,,,4080.0000000,1.0000000,,,,,,0E-7 +346ee1d2fcf7f70c,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +f77b84ee3fc05e8c,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,samtools_fixmate/1.9,,,,4080.0000000,1.0000000,,,,,,0E-7 +c1f53f965e3f11fc,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +3b076214a691ebd7,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,samtools_fixmate/1.9,,,,4080.0000000,1.0000000,,,,,,0E-7 +9e22d11eadbf9087,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +873462c21322a5f4,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,trimmomatic/0.38.1,,,,12884.0000000,6.0000000,,,,,,0E-7 +03ea2d9f5a73c06f,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +4e6201563fcf9362,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +3e0e92ef37a541d1,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,trimmomatic/0.38.1,,,,12884.0000000,6.0000000,,,,,,1.0000000 +14174cb4b325ed48,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +4ec971aa3f08aa41,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +da2d40552de3029b,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,error,trimmomatic/0.38.1,,,,,,,,,,, +7fd0ebaa51c36236,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +fe9a443ac2bf50b7,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,trimmomatic/0.38.1,,,,12884.0000000,6.0000000,,,,,,1.0000000 +f8ff9528d950258c,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +f7e63bf4200f2b12,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +64262c26ef4b4f8c,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,error,upload1,,,,,,,,,,, +78f113974806f741,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +877faa65ca7adf3a,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,error,upload1,,,,,,,,,,, +9bada2958fd12d58,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,trimmomatic/0.38.1,,,,12884.0000000,6.0000000,,,,,,0E-7 +9d1e19ed450e6c86,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +010a92ede45bd68a,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +a6000a46566a855e,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,error,upload1,,,,,,,,,,, +87943a4e2dd4167e,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,trimmomatic/0.38.1,,,,12884.0000000,6.0000000,,,,,,1.0000000 +b4ed4b13837a07b8,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +8b6f5ce3aa2377af,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +584d0aa45b50556b,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,trimmomatic/0.38.1,,,,12884.0000000,6.0000000,,,,,,0E-7 +4a12ddb120e74961,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +c0c8a69c8070f677,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +7bf7e48be40dc04d,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,trimmomatic/0.38.1,,,,12884.0000000,6.0000000,,,,,,0E-7 +0c8c289d788b4c08,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +defb5211a6a94aa8,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +fe0a9ea15b54bf6c,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,error,upload1,,,,,,,,,,, +a57289ad4f175228,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,trimmomatic/0.38.1,,,,12884.0000000,6.0000000,,,,,,0E-7 +49702c00cc3a3629,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,3.0000000 +3ec05b8c179927a5,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,datamash_reverse/1.8+galaxy0,,,,4080.0000000,1.0000000,,,,,,0E-7 +24323ccc9ba4a0ff,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +a66ef6e4a4a0e1d4,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,annotatemyids/3.5.0.1,,,,4080.0000000,1.0000000,,,,,,18.0000000 +f560f43330980975,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +cf4669e3d1f60b4e,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,annotatemyids/3.5.0.1,,,,4080.0000000,1.0000000,,,,,,18.0000000 +e39ca091cf5339f4,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +ef71afcbd5eac7e6,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,annotatemyids/3.5.0.1,,,,4080.0000000,1.0000000,,,,,,17.0000000 +198a4099c8492732,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 +a21c742fb7f71c24,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,annotatemyids/3.5.0.1,,,,4080.0000000,1.0000000,,,,,,17.0000000 +ed165837e8ba4cca,ed165837e8ba4cca,anvil-test-2024-09-14-00-47,ok,upload1,,,,4080.0000000,1.0000000,,,,,,4.0000000 diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/job.log b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/job.log new file mode 100644 index 000000000..64881fcd8 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/job.log @@ -0,0 +1,4029 @@ +galaxy.jobs.handler DEBUG 2024-09-14 00:50:31,099 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 5 +tpv.core.entities DEBUG 2024-09-14 00:50:31,124 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:50:31,124 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:50:31,128 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:50:31,141 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:50:31,156 [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 2024-09-14 00:50:31,161 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [5] queued (33.322 ms) +galaxy.jobs.handler INFO 2024-09-14 00:50:31,164 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (5) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:50:31,168 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 5 +galaxy.jobs DEBUG 2024-09-14 00:50:31,253 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [5] prepared (69.009 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:50:31,272 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '6:/galaxy/server/database/objects/f/e/6/dataset_fe681ec1-6341-4ff3-91be-67bab7337de5_files:/galaxy/server/database/objects/f/e/6/dataset_fe681ec1-6341-4ff3-91be-67bab7337de5.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:50:31,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:50:40,404 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 5: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:50:45,071 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 5 finished +galaxy.model.metadata DEBUG 2024-09-14 00:50:45,119 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 6 +galaxy.jobs INFO 2024-09-14 00:50:45,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 5 in /galaxy/server/database/jobs_directory/000/5 +galaxy.jobs DEBUG 2024-09-14 00:50:45,198 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 5 executed (104.966 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:50:46,510 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 6 +tpv.core.entities DEBUG 2024-09-14 00:50:46,542 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:50:46,543 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:50:46,548 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:50:46,562 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:50:46,578 [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 2024-09-14 00:50:46,584 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [6] queued (35.817 ms) +galaxy.jobs.handler INFO 2024-09-14 00:50:46,587 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (6) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:50:46,591 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 6 +galaxy.jobs DEBUG 2024-09-14 00:50:46,664 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [6] prepared (57.870 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:50:46,664 [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 2024-09-14 00:50:46,664 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1: mulled-v2-fbf0980300c3eec60801bb7996eb16010c38939d:ac85adae9385b3d083688aab93961c503a6f572b +galaxy.tool_util.deps.containers INFO 2024-09-14 00:50:46,680 [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-fbf0980300c3eec60801bb7996eb16010c38939d:ac85adae9385b3d083688aab93961c503a6f572b-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:50:46,698 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/6/tool_script.sh] for tool command [echo $(R --version | grep version | grep -v GNU)", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dr.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ") > /galaxy/server/database/jobs_directory/000/6/outputs/COMMAND_VERSION 2>&1; +Rscript '/galaxy/server/database/jobs_directory/000/6/configs/tmpuk790mlu'] +galaxy.jobs.runners DEBUG 2024-09-14 00:50:46,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (6) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/6/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/6/galaxy_6.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/6/working/"*".tab" ] ; then cp "/galaxy/server/database/jobs_directory/000/6/working/"*".tab" "/galaxy/server/database/objects/2/1/c/dataset_21c89c91-f995-459e-b47e-d2e33ae3547e.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:50:46,719 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:50:46,719 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1: mulled-v2-fbf0980300c3eec60801bb7996eb16010c38939d:ac85adae9385b3d083688aab93961c503a6f572b +galaxy.tool_util.deps.containers INFO 2024-09-14 00:50:46,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fbf0980300c3eec60801bb7996eb16010c38939d:ac85adae9385b3d083688aab93961c503a6f572b-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:51:08,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 6: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:51:13,419 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 6 finished +galaxy.model.metadata DEBUG 2024-09-14 00:51:13,470 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 7 +galaxy.jobs INFO 2024-09-14 00:51:13,498 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 6 in /galaxy/server/database/jobs_directory/000/6 +galaxy.objectstore CRITICAL 2024-09-14 00:51:13,537 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'tmpuk790mlu' +galaxy.jobs DEBUG 2024-09-14 00:51:13,538 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 6 executed (94.557 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:51:16,149 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 7 +tpv.core.entities DEBUG 2024-09-14 00:51:16,176 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:51:16,177 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:51:16,180 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:51:16,193 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:51:16,208 [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 2024-09-14 00:51:16,214 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [7] queued (33.394 ms) +galaxy.jobs.handler INFO 2024-09-14 00:51:16,216 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (7) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:51:16,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 7 +galaxy.jobs DEBUG 2024-09-14 00:51:16,302 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [7] prepared (67.090 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:51:16,320 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '8:/galaxy/server/database/objects/5/9/4/dataset_594ce8d3-34d3-4e83-ba57-7f6cd4a922d3_files:/galaxy/server/database/objects/5/9/4/dataset_594ce8d3-34d3-4e83-ba57-7f6cd4a922d3.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:51:16,330 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:51:25,017 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 7: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:51:29,849 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 7 finished +galaxy.model.metadata DEBUG 2024-09-14 00:51:29,897 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 8 +galaxy.jobs INFO 2024-09-14 00:51:29,931 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 7 in /galaxy/server/database/jobs_directory/000/7 +galaxy.jobs DEBUG 2024-09-14 00:51:29,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 7 executed (108.552 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:51:30,476 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 8 +tpv.core.entities DEBUG 2024-09-14 00:51:30,505 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:51:30,506 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:51:30,509 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:51:30,523 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:51:30,536 [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 2024-09-14 00:51:30,542 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [8] queued (32.672 ms) +galaxy.jobs.handler INFO 2024-09-14 00:51:30,545 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (8) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:51:30,549 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 8 +galaxy.jobs DEBUG 2024-09-14 00:51:30,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [8] prepared (50.597 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:51:30,615 [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 2024-09-14 00:51:30,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1: mulled-v2-fbf0980300c3eec60801bb7996eb16010c38939d:ac85adae9385b3d083688aab93961c503a6f572b +galaxy.tool_util.deps.containers INFO 2024-09-14 00:51:30,633 [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-fbf0980300c3eec60801bb7996eb16010c38939d:ac85adae9385b3d083688aab93961c503a6f572b-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:51:30,653 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/8/tool_script.sh] for tool command [echo $(R --version | grep version | grep -v GNU)", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dr.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ") > /galaxy/server/database/jobs_directory/000/8/outputs/COMMAND_VERSION 2>&1; +Rscript '/galaxy/server/database/jobs_directory/000/8/configs/tmpfbw71315'] +galaxy.jobs.runners DEBUG 2024-09-14 00:51:30,665 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (8) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/8/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/8/galaxy_8.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/8/working/"*".tab" ] ; then cp "/galaxy/server/database/jobs_directory/000/8/working/"*".tab" "/galaxy/server/database/objects/1/6/f/dataset_16f94c91-8c43-4524-988d-4e562228ca48.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:51:30,676 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:51:30,676 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1: mulled-v2-fbf0980300c3eec60801bb7996eb16010c38939d:ac85adae9385b3d083688aab93961c503a6f572b +galaxy.tool_util.deps.containers INFO 2024-09-14 00:51:30,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-fbf0980300c3eec60801bb7996eb16010c38939d:ac85adae9385b3d083688aab93961c503a6f572b-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:51:53,549 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 8: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:51:58,117 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 8 finished +galaxy.model.metadata DEBUG 2024-09-14 00:51:58,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 9 +galaxy.jobs INFO 2024-09-14 00:51:58,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 8 in /galaxy/server/database/jobs_directory/000/8 +galaxy.objectstore CRITICAL 2024-09-14 00:51:58,229 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'tmpfbw71315' +galaxy.jobs DEBUG 2024-09-14 00:51:58,229 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 8 executed (89.850 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:52:02,139 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 9 +tpv.core.entities DEBUG 2024-09-14 00:52:02,171 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:52:02,171 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:52:02,176 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:52:02,188 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:52:02,204 [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 2024-09-14 00:52:02,211 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [9] queued (35.468 ms) +galaxy.jobs.handler INFO 2024-09-14 00:52:02,215 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (9) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:52:02,218 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 9 +galaxy.jobs DEBUG 2024-09-14 00:52:02,304 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [9] prepared (70.828 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:52:02,321 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/9/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/9/registry.xml' '/galaxy/server/database/jobs_directory/000/9/upload_params.json' '10:/galaxy/server/database/objects/8/f/a/dataset_8faa6cfe-41d6-4761-91ed-4863eaa406f4_files:/galaxy/server/database/objects/8/f/a/dataset_8faa6cfe-41d6-4761-91ed-4863eaa406f4.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:52:02,332 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (9) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/9/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/9/galaxy_9.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:52:09,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 9: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:52:14,510 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 9 finished +galaxy.model.metadata DEBUG 2024-09-14 00:52:14,563 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 10 +galaxy.jobs INFO 2024-09-14 00:52:14,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 9 in /galaxy/server/database/jobs_directory/000/9 +galaxy.jobs DEBUG 2024-09-14 00:52:14,655 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 9 executed (120.513 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:52:15,465 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 10 +tpv.core.entities DEBUG 2024-09-14 00:52:15,503 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:52:15,504 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:52:15,511 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:52:15,528 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:52:15,548 [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 2024-09-14 00:52:15,555 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [10] queued (44.314 ms) +galaxy.jobs.handler INFO 2024-09-14 00:52:15,558 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (10) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:52:15,562 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 10 +galaxy.jobs DEBUG 2024-09-14 00:52:15,632 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [10] prepared (52.371 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:52:15,632 [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 2024-09-14 00:52:15,632 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0: datamash:1.8 +galaxy.tool_util.deps.containers INFO 2024-09-14 00:52:15,799 [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/datamash:1.8,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:52:15,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/10/tool_script.sh] for tool command [datamash reverse < /galaxy/server/database/objects/8/f/a/dataset_8faa6cfe-41d6-4761-91ed-4863eaa406f4.dat > /galaxy/server/database/objects/e/f/b/dataset_efb893ad-c264-445f-a823-63734f94805f.dat] +galaxy.jobs.runners DEBUG 2024-09-14 00:52:15,831 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (10) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/10/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/10/galaxy_10.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:52:15,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:52:15,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0: datamash:1.8 +galaxy.tool_util.deps.containers INFO 2024-09-14 00:52:15,858 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/datamash:1.8,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:52:22,992 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 10: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:52:27,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 10 finished +galaxy.model.metadata DEBUG 2024-09-14 00:52:27,873 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 11 +galaxy.jobs INFO 2024-09-14 00:52:27,909 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 10 in /galaxy/server/database/jobs_directory/000/10 +galaxy.jobs DEBUG 2024-09-14 00:52:27,958 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 10 executed (114.196 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:52:31,891 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 11 +tpv.core.entities DEBUG 2024-09-14 00:52:31,928 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:52:31,929 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:52:31,934 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:52:31,949 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:52:31,964 [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 2024-09-14 00:52:31,970 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [11] queued (35.239 ms) +galaxy.jobs.handler INFO 2024-09-14 00:52:31,973 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (11) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:52:31,978 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 11 +galaxy.jobs DEBUG 2024-09-14 00:52:32,082 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [11] prepared (86.333 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:52:32,102 [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' '12:/galaxy/server/database/objects/7/3/e/dataset_73eedd44-ddbb-4f2d-8dde-5dfd5a60c948_files:/galaxy/server/database/objects/7/3/e/dataset_73eedd44-ddbb-4f2d-8dde-5dfd5a60c948.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:52:32,115 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:52:40,210 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 11: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:52:45,055 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 11 finished +galaxy.model.metadata DEBUG 2024-09-14 00:52:45,108 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 12 +galaxy.jobs INFO 2024-09-14 00:52:45,144 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 11 in /galaxy/server/database/jobs_directory/000/11 +galaxy.jobs DEBUG 2024-09-14 00:52:45,198 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 11 executed (118.465 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:52:46,309 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 12 +tpv.core.entities DEBUG 2024-09-14 00:52:46,341 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/pjbriggs/trimmomatic/trimmomatic/.*, abstract=False, cores=6, mem=12, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[{'name': '_JAVA_OPTIONS', 'value': '-Xmx{int(mem)}G -Xms1G'}], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:52:46,341 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:52:46,346 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:52:46,360 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:52:46,383 [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 2024-09-14 00:52:46,391 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [12] queued (44.449 ms) +galaxy.jobs.handler INFO 2024-09-14 00:52:46,394 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (12) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:52:46,399 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 12 +galaxy.jobs DEBUG 2024-09-14 00:52:46,509 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [12] prepared (92.596 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:52:46,510 [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 2024-09-14 00:52:46,510 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:52:46,687 [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-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:52:46,706 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/12/tool_script.sh] for tool command [if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/7/3/e/dataset_73eedd44-ddbb-4f2d-8dde-5dfd5a60c948.dat' fastq_in.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger' fastq_out.'fastqsanger' SLIDINGWINDOW:4:20 -trimlog trimlog 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger' '/galaxy/server/database/objects/3/5/a/dataset_35ab1889-5e9b-4f85-984d-7ac85d5d87af.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:52:46,727 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (12) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/12/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/12/galaxy_12.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/12/working/trimlog" ] ; then cp "/galaxy/server/database/jobs_directory/000/12/working/trimlog" "/galaxy/server/database/objects/c/f/2/dataset_cf220079-4323-49eb-9ac7-0a9883096b20.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/12/working/trimmomatic.log" ] ; then cp "/galaxy/server/database/jobs_directory/000/12/working/trimmomatic.log" "/galaxy/server/database/objects/a/a/9/dataset_aa92a19e-03d0-4938-a23c-88c25d7ae205.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:52:46,739 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:52:46,739 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:52:46,756 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:53:05,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 12: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:53:10,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 12 finished +galaxy.model.metadata DEBUG 2024-09-14 00:53:10,725 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 13 +galaxy.model.metadata DEBUG 2024-09-14 00:53:10,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 14 +galaxy.model.metadata DEBUG 2024-09-14 00:53:10,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 15 +galaxy.util WARNING 2024-09-14 00:53:10,754 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/3/5/a/dataset_35ab1889-5e9b-4f85-984d-7ac85d5d87af.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/3/5/a/dataset_35ab1889-5e9b-4f85-984d-7ac85d5d87af.dat' +galaxy.jobs INFO 2024-09-14 00:53:10,787 [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.objectstore CRITICAL 2024-09-14 00:53:10,837 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmpuvdw9znp' +galaxy.jobs DEBUG 2024-09-14 00:53:10,838 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 12 executed (145.422 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:53:15,040 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 13 +tpv.core.entities DEBUG 2024-09-14 00:53:15,078 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:53:15,078 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:53:15,083 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:53:15,098 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:53:15,121 [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 2024-09-14 00:53:15,128 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [13] queued (45.058 ms) +galaxy.jobs.handler INFO 2024-09-14 00:53:15,132 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (13) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:53:15,137 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 13 +galaxy.jobs DEBUG 2024-09-14 00:53:15,235 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [13] prepared (80.032 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:53:15,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/13/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/13/registry.xml' '/galaxy/server/database/jobs_directory/000/13/upload_params.json' '16:/galaxy/server/database/objects/d/d/7/dataset_dd7cfbb0-f7a0-489a-868d-01808f00a8fd_files:/galaxy/server/database/objects/d/d/7/dataset_dd7cfbb0-f7a0-489a-868d-01808f00a8fd.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:53:15,266 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 ERROR 2024-09-14 00:53:22,931 [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/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.108.80.1:443/apis/batch/v1/namespaces/prod-24-09-14-00-32-1/jobs/gxy-rzcrg + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-rzcrg": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:53:22,975 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (13/gxy-rzcrg) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-09-14 00:53:24,322 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 14 +tpv.core.entities DEBUG 2024-09-14 00:53:24,357 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:53:24,357 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:53:24,363 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:53:24,377 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:53:24,393 [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 2024-09-14 00:53:24,399 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [14] queued (36.192 ms) +galaxy.jobs.handler INFO 2024-09-14 00:53:24,402 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (14) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:53:24,407 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 14 +galaxy.jobs DEBUG 2024-09-14 00:53:24,506 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [14] prepared (80.328 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:53:24,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/14/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/14/registry.xml' '/galaxy/server/database/jobs_directory/000/14/upload_params.json' '17:/galaxy/server/database/objects/5/3/5/dataset_53530603-4b11-4771-b00f-55b679cdffef_files:/galaxy/server/database/objects/5/3/5/dataset_53530603-4b11-4771-b00f-55b679cdffef.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:53:24,542 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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.handler DEBUG 2024-09-14 00:53:25,405 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 15 +tpv.core.entities DEBUG 2024-09-14 00:53:25,437 [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=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:53:25,437 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:53:25,442 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:53:25,461 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:53:25,479 [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 2024-09-14 00:53:25,485 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [15] queued (43.269 ms) +galaxy.jobs.handler INFO 2024-09-14 00:53:25,489 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (15) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:53:25,494 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 15 +galaxy.jobs DEBUG 2024-09-14 00:53:25,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [15] prepared (79.938 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:53:25,616 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '18:/galaxy/server/database/objects/3/7/6/dataset_376767a6-2c00-4bc6-9292-29286bacc97d_files:/galaxy/server/database/objects/3/7/6/dataset_376767a6-2c00-4bc6-9292-29286bacc97d.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:53:25,629 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:53:32,701 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 14: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:53:33,848 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 15: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:53:37,602 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 14 finished +galaxy.model.metadata DEBUG 2024-09-14 00:53:37,655 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 17 +galaxy.jobs INFO 2024-09-14 00:53:37,690 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 14 in /galaxy/server/database/jobs_directory/000/14 +galaxy.jobs DEBUG 2024-09-14 00:53:37,738 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 14 executed (112.878 ms) +galaxy.jobs.runners DEBUG 2024-09-14 00:53:38,654 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 15 finished +galaxy.model.metadata DEBUG 2024-09-14 00:53:38,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 18 +galaxy.jobs INFO 2024-09-14 00:53:38,806 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 15 in /galaxy/server/database/jobs_directory/000/15 +galaxy.jobs DEBUG 2024-09-14 00:53:38,863 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 15 executed (150.214 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:53:39,927 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 16 +tpv.core.entities DEBUG 2024-09-14 00:53:39,969 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/pjbriggs/trimmomatic/trimmomatic/.*, abstract=False, cores=6, mem=12, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[{'name': '_JAVA_OPTIONS', 'value': '-Xmx{int(mem)}G -Xms1G'}], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:53:39,970 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:53:39,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:53:39,993 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:53:40,020 [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 2024-09-14 00:53:40,030 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [16] queued (52.133 ms) +galaxy.jobs.handler INFO 2024-09-14 00:53:40,035 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (16) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:53:40,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 16 +galaxy.jobs DEBUG 2024-09-14 00:53:40,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [16] prepared (71.079 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:53:40,125 [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 2024-09-14 00:53:40,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:53:40,144 [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-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:53:40,165 [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 [if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/5/3/5/dataset_53530603-4b11-4771-b00f-55b679cdffef.dat' fastq_r1.'fastqsanger.gz' && ln -s '/galaxy/server/database/objects/3/7/6/dataset_376767a6-2c00-4bc6-9292-29286bacc97d.dat' fastq_r2.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar PE -threads ${GALAXY_SLOTS:-6} fastq_r1.'fastqsanger.gz' fastq_r2.'fastqsanger.gz' fastq_out_r1_paired.'fastqsanger.gz' fastq_out_r1_unpaired.'fastqsanger.gz' fastq_out_r2_paired.'fastqsanger.gz' fastq_out_r2_unpaired.'fastqsanger.gz' SLIDINGWINDOW:4:20 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out_r1_paired.'fastqsanger.gz' '/galaxy/server/database/objects/f/3/d/dataset_f3d1ff58-dc18-49db-b4e4-db6176e0218b.dat' && mv fastq_out_r1_unpaired.'fastqsanger.gz' '/galaxy/server/database/objects/f/5/0/dataset_f50f33ad-1d07-4f0d-b25a-a7f8da385242.dat' && mv fastq_out_r2_paired.'fastqsanger.gz' '/galaxy/server/database/objects/3/9/1/dataset_391d572f-5ab9-4e2e-9ee3-ab4992b86b14.dat' && mv fastq_out_r2_unpaired.'fastqsanger.gz' '/galaxy/server/database/objects/7/3/8/dataset_738b4cb6-8c7c-41cf-978d-c535b76e59a5.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:53:40,194 [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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:53:40,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:53:40,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:53:40,224 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:53:45,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 16: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:53:50,069 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 16 finished +galaxy.model.metadata DEBUG 2024-09-14 00:53:50,130 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 19 +galaxy.model.metadata DEBUG 2024-09-14 00:53:50,141 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 20 +galaxy.model.metadata DEBUG 2024-09-14 00:53:50,153 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 21 +galaxy.model.metadata DEBUG 2024-09-14 00:53:50,165 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 22 +galaxy.util WARNING 2024-09-14 00:53:50,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/f/3/d/dataset_f3d1ff58-dc18-49db-b4e4-db6176e0218b.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/f/3/d/dataset_f3d1ff58-dc18-49db-b4e4-db6176e0218b.dat' +galaxy.util WARNING 2024-09-14 00:53:50,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/3/9/1/dataset_391d572f-5ab9-4e2e-9ee3-ab4992b86b14.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/3/9/1/dataset_391d572f-5ab9-4e2e-9ee3-ab4992b86b14.dat' +galaxy.util WARNING 2024-09-14 00:53:50,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/f/5/0/dataset_f50f33ad-1d07-4f0d-b25a-a7f8da385242.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/f/5/0/dataset_f50f33ad-1d07-4f0d-b25a-a7f8da385242.dat' +galaxy.util WARNING 2024-09-14 00:53:50,177 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/7/3/8/dataset_738b4cb6-8c7c-41cf-978d-c535b76e59a5.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/7/3/8/dataset_738b4cb6-8c7c-41cf-978d-c535b76e59a5.dat' +galaxy.jobs INFO 2024-09-14 00:53:50,211 [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.objectstore CRITICAL 2024-09-14 00:53:50,266 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'tmpuq3dymqu' +galaxy.jobs DEBUG 2024-09-14 00:53:50,266 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 16 executed (171.682 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:53:55,394 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 17, 18 +tpv.core.entities DEBUG 2024-09-14 00:53:55,427 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:53:55,428 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:53:55,432 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:53:55,448 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:53:55,466 [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 2024-09-14 00:53:55,472 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [17] queued (40.600 ms) +galaxy.jobs.handler INFO 2024-09-14 00:53:55,476 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (17) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:53:55,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 17 +tpv.core.entities DEBUG 2024-09-14 00:53:55,493 [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=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:53:55,494 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:53:55,500 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:53:55,519 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:53:55,551 [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 2024-09-14 00:53:55,562 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [18] queued (61.371 ms) +galaxy.jobs.handler INFO 2024-09-14 00:53:55,567 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (18) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:53:55,572 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 18 +galaxy.jobs DEBUG 2024-09-14 00:53:55,598 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [17] prepared (96.389 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:53:55,624 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '23:/galaxy/server/database/objects/a/3/9/dataset_a399456d-910b-4145-8d59-78d9823e55eb_files:/galaxy/server/database/objects/a/3/9/dataset_a399456d-910b-4145-8d59-78d9823e55eb.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:53:55,646 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (17) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/17/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/17/galaxy_17.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-09-14 00:53:55,700 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [18] prepared (108.063 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:53:55,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/18/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/18/registry.xml' '/galaxy/server/database/jobs_directory/000/18/upload_params.json' '24:/galaxy/server/database/objects/9/7/6/dataset_9761247d-c9ae-48df-900f-53bd8cc116f1_files:/galaxy/server/database/objects/9/7/6/dataset_9761247d-c9ae-48df-900f-53bd8cc116f1.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:53:55,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (18) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/18/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/18/galaxy_18.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:54:03,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 17: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:54:03,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 18: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:54:08,345 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 17 finished +galaxy.model.metadata DEBUG 2024-09-14 00:54:08,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 23 +galaxy.jobs INFO 2024-09-14 00:54:08,439 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 17 in /galaxy/server/database/jobs_directory/000/17 +galaxy.jobs DEBUG 2024-09-14 00:54:08,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 17 executed (120.618 ms) +galaxy.jobs.runners DEBUG 2024-09-14 00:54:08,494 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 18 finished +galaxy.model.metadata DEBUG 2024-09-14 00:54:08,553 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 24 +galaxy.jobs INFO 2024-09-14 00:54:08,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 18 in /galaxy/server/database/jobs_directory/000/18 +galaxy.jobs DEBUG 2024-09-14 00:54:08,649 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 18 executed (127.231 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:54:09,856 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 19 +tpv.core.entities DEBUG 2024-09-14 00:54:09,887 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/pjbriggs/trimmomatic/trimmomatic/.*, abstract=False, cores=6, mem=12, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[{'name': '_JAVA_OPTIONS', 'value': '-Xmx{int(mem)}G -Xms1G'}], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:54:09,887 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:54:09,891 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:54:09,908 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:54:09,935 [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 2024-09-14 00:54:09,942 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [19] queued (50.152 ms) +galaxy.jobs.handler INFO 2024-09-14 00:54:09,945 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (19) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:54:09,950 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 19 +galaxy.jobs DEBUG 2024-09-14 00:54:10,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [19] prepared (74.758 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:54:10,046 [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 2024-09-14 00:54:10,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:54:10,227 [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-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:54:10,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/19/tool_script.sh] for tool command [if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/a/3/9/dataset_a399456d-910b-4145-8d59-78d9823e55eb.dat' fastq_r1.'fastqsanger' && ln -s '/galaxy/server/database/objects/9/7/6/dataset_9761247d-c9ae-48df-900f-53bd8cc116f1.dat' fastq_r2.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar PE -threads ${GALAXY_SLOTS:-6} fastq_r1.'fastqsanger' fastq_r2.'fastqsanger' fastq_out_r1_paired.'fastqsanger' fastq_out_r1_unpaired.'fastqsanger' fastq_out_r2_paired.'fastqsanger' fastq_out_r2_unpaired.'fastqsanger' SLIDINGWINDOW:4:20 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out_r1_paired.'fastqsanger' '/galaxy/server/database/objects/f/4/9/dataset_f49461db-2aa7-4951-a7f8-5f1de529a7ba.dat' && mv fastq_out_r1_unpaired.'fastqsanger' '/galaxy/server/database/objects/e/e/8/dataset_ee808beb-2d67-4978-9f04-282d366f017a.dat' && mv fastq_out_r2_paired.'fastqsanger' '/galaxy/server/database/objects/9/c/e/dataset_9ce668de-b481-4e51-8d19-82fbcc93e8c9.dat' && mv fastq_out_r2_unpaired.'fastqsanger' '/galaxy/server/database/objects/c/d/e/dataset_cde3d066-4d48-4554-8895-ec108140037e.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:54:10,276 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (19) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/19/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/19/galaxy_19.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:54:10,289 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:54:10,289 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:54:10,307 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:54:14,748 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 19: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:54:19,544 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 19 finished +galaxy.model.metadata DEBUG 2024-09-14 00:54:19,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 25 +galaxy.model.metadata DEBUG 2024-09-14 00:54:19,603 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 26 +galaxy.model.metadata DEBUG 2024-09-14 00:54:19,632 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 27 +galaxy.model.metadata DEBUG 2024-09-14 00:54:19,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 28 +galaxy.util WARNING 2024-09-14 00:54:19,670 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/f/4/9/dataset_f49461db-2aa7-4951-a7f8-5f1de529a7ba.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/f/4/9/dataset_f49461db-2aa7-4951-a7f8-5f1de529a7ba.dat' +galaxy.util WARNING 2024-09-14 00:54:19,671 [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/9/c/e/dataset_9ce668de-b481-4e51-8d19-82fbcc93e8c9.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/9/c/e/dataset_9ce668de-b481-4e51-8d19-82fbcc93e8c9.dat' +galaxy.util WARNING 2024-09-14 00:54:19,671 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/e/8/dataset_ee808beb-2d67-4978-9f04-282d366f017a.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/e/8/dataset_ee808beb-2d67-4978-9f04-282d366f017a.dat' +galaxy.util WARNING 2024-09-14 00:54:19,671 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/d/e/dataset_cde3d066-4d48-4554-8895-ec108140037e.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/d/e/dataset_cde3d066-4d48-4554-8895-ec108140037e.dat' +galaxy.jobs INFO 2024-09-14 00:54:19,699 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 19 in /galaxy/server/database/jobs_directory/000/19 +galaxy.objectstore CRITICAL 2024-09-14 00:54:19,739 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'tmpjnc0o6y1' +galaxy.jobs DEBUG 2024-09-14 00:54:19,740 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 19 executed (172.662 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:54:24,225 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 20 +tpv.core.entities DEBUG 2024-09-14 00:54:24,254 [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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:54:24,255 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:54:24,259 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:54:24,272 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:54:24,287 [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 2024-09-14 00:54:24,293 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [20] queued (33.553 ms) +galaxy.jobs.handler INFO 2024-09-14 00:54:24,296 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (20) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:54:24,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 20 +galaxy.jobs DEBUG 2024-09-14 00:54:24,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [20] prepared (72.894 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:54:24,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/20/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/20/registry.xml' '/galaxy/server/database/jobs_directory/000/20/upload_params.json' '29:/galaxy/server/database/objects/a/7/5/dataset_a754df7e-7666-4963-9680-c1eb2b89c689_files:/galaxy/server/database/objects/a/7/5/dataset_a754df7e-7666-4963-9680-c1eb2b89c689.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:54:24,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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.handler DEBUG 2024-09-14 00:54:25,299 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 21 +tpv.core.entities DEBUG 2024-09-14 00:54:25,331 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:54:25,332 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:54:25,336 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:54:25,350 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:54:25,367 [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 2024-09-14 00:54:25,374 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [21] queued (37.956 ms) +galaxy.jobs.handler INFO 2024-09-14 00:54:25,378 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (21) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:54:25,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 21 +galaxy.jobs DEBUG 2024-09-14 00:54:25,473 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [21] prepared (76.823 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:54:25,492 [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' '30:/galaxy/server/database/objects/8/5/8/dataset_858a76de-2a92-4830-bf20-150923ad3cee_files:/galaxy/server/database/objects/8/5/8/dataset_858a76de-2a92-4830-bf20-150923ad3cee.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:54:25,502 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:54:40,907 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 20: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:54:40,931 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 21: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:54:45,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 20 finished +galaxy.jobs.runners DEBUG 2024-09-14 00:54:45,698 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 21 finished +galaxy.model.metadata DEBUG 2024-09-14 00:54:45,746 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 29 +galaxy.model.metadata DEBUG 2024-09-14 00:54:45,747 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 30 +galaxy.jobs INFO 2024-09-14 00:54:45,790 [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 INFO 2024-09-14 00:54:45,793 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 21 in /galaxy/server/database/jobs_directory/000/21 +galaxy.jobs DEBUG 2024-09-14 00:54:45,841 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 20 executed (125.066 ms) +galaxy.jobs DEBUG 2024-09-14 00:54:45,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 21 executed (124.093 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:54:46,787 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 22 +tpv.core.entities DEBUG 2024-09-14 00:54:46,824 [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/pjbriggs/trimmomatic/trimmomatic/.*, abstract=False, cores=6, mem=12, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[{'name': '_JAVA_OPTIONS', 'value': '-Xmx{int(mem)}G -Xms1G'}], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:54:46,824 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:54:46,829 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:54:46,842 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:54:46,866 [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 2024-09-14 00:54:46,875 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [22] queued (46.392 ms) +galaxy.jobs.handler INFO 2024-09-14 00:54:46,879 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (22) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:54:46,883 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 22 +galaxy.jobs DEBUG 2024-09-14 00:54:46,968 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [22] prepared (67.704 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:54:46,969 [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 2024-09-14 00:54:46,969 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:54:46,989 [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-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:54:47,012 [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 [if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/a/7/5/dataset_a754df7e-7666-4963-9680-c1eb2b89c689.dat' fastq_r1.'fastqillumina' && ln -s '/galaxy/server/database/objects/8/5/8/dataset_858a76de-2a92-4830-bf20-150923ad3cee.dat' fastq_r2.'fastqillumina' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar PE -threads ${GALAXY_SLOTS:-6} fastq_r1.'fastqillumina' fastq_r2.'fastqillumina' fastq_out_r1_paired.'fastqillumina' fastq_out_r1_unpaired.'fastqillumina' fastq_out_r2_paired.'fastqillumina' fastq_out_r2_unpaired.'fastqillumina' SLIDINGWINDOW:4:20 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out_r1_paired.'fastqillumina' '/galaxy/server/database/objects/e/6/f/dataset_e6f68f70-9838-4b6c-9ab8-4d2f4ece8862.dat' && mv fastq_out_r1_unpaired.'fastqillumina' '/galaxy/server/database/objects/c/6/d/dataset_c6d8a8b3-4385-4bce-b0a1-1f6a777cbd6c.dat' && mv fastq_out_r2_paired.'fastqillumina' '/galaxy/server/database/objects/9/e/6/dataset_9e625eef-b2f0-4558-a53d-9ad9c770a633.dat' && mv fastq_out_r2_unpaired.'fastqillumina' '/galaxy/server/database/objects/d/1/d/dataset_d1de5762-2fca-4023-a70d-97380dd0d639.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:54:47,041 [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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:54:47,054 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:54:47,054 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:54:47,071 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:54:52,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 22: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:54:56,693 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 22 finished +galaxy.model.metadata DEBUG 2024-09-14 00:54:56,746 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 31 +galaxy.model.metadata DEBUG 2024-09-14 00:54:56,755 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 32 +galaxy.model.metadata DEBUG 2024-09-14 00:54:56,784 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 33 +galaxy.model.metadata DEBUG 2024-09-14 00:54:56,817 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 34 +galaxy.util WARNING 2024-09-14 00:54:56,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/6/f/dataset_e6f68f70-9838-4b6c-9ab8-4d2f4ece8862.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/6/f/dataset_e6f68f70-9838-4b6c-9ab8-4d2f4ece8862.dat' +galaxy.util WARNING 2024-09-14 00:54:56,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/9/e/6/dataset_9e625eef-b2f0-4558-a53d-9ad9c770a633.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/9/e/6/dataset_9e625eef-b2f0-4558-a53d-9ad9c770a633.dat' +galaxy.util WARNING 2024-09-14 00:54:56,825 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/6/d/dataset_c6d8a8b3-4385-4bce-b0a1-1f6a777cbd6c.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/6/d/dataset_c6d8a8b3-4385-4bce-b0a1-1f6a777cbd6c.dat' +galaxy.util WARNING 2024-09-14 00:54:56,825 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/d/1/d/dataset_d1de5762-2fca-4023-a70d-97380dd0d639.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/d/1/d/dataset_d1de5762-2fca-4023-a70d-97380dd0d639.dat' +galaxy.jobs INFO 2024-09-14 00:54:56,855 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 22 in /galaxy/server/database/jobs_directory/000/22 +galaxy.objectstore CRITICAL 2024-09-14 00:54:56,898 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'tmpfqwz9v1b' +galaxy.jobs DEBUG 2024-09-14 00:54:56,898 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 22 executed (182.165 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:55:01,248 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 23 +tpv.core.entities DEBUG 2024-09-14 00:55:01,274 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:55:01,275 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:55:01,278 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:55:01,290 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:55:01,304 [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 2024-09-14 00:55:01,310 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [23] queued (31.302 ms) +galaxy.jobs.handler INFO 2024-09-14 00:55:01,313 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (23) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:55:01,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 23 +galaxy.jobs DEBUG 2024-09-14 00:55:01,409 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [23] prepared (77.384 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:55:01,429 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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' '35:/galaxy/server/database/objects/b/c/d/dataset_bcda9236-4541-4155-8ce6-4c842913f7b4_files:/galaxy/server/database/objects/b/c/d/dataset_bcda9236-4541-4155-8ce6-4c842913f7b4.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:55:01,440 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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.handler DEBUG 2024-09-14 00:55:02,315 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 24 +tpv.core.entities DEBUG 2024-09-14 00:55:02,342 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:55:02,342 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:55:02,346 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:55:02,357 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:55:02,369 [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 2024-09-14 00:55:02,375 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [24] queued (29.491 ms) +galaxy.jobs.handler INFO 2024-09-14 00:55:02,379 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (24) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:55:02,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 24 +galaxy.jobs DEBUG 2024-09-14 00:55:02,466 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [24] prepared (70.988 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:55:02,483 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/24/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/24/registry.xml' '/galaxy/server/database/jobs_directory/000/24/upload_params.json' '36:/galaxy/server/database/objects/e/c/7/dataset_ec7b65f2-1093-405b-9cc9-3f438d77c704_files:/galaxy/server/database/objects/e/c/7/dataset_ec7b65f2-1093-405b-9cc9-3f438d77c704.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:55:02,495 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (24) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/24/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/24/galaxy_24.ec; sh -c "exit $return_code" +galaxy.jobs.runners.kubernetes ERROR 2024-09-14 00:55:09,343 [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/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.108.80.1:443/apis/batch/v1/namespaces/prod-24-09-14-00-32-1/jobs/gxy-sf4nz + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-sf4nz": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:55:09,381 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (23/gxy-sf4nz) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-09-14 00:55:10,505 [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.handler DEBUG 2024-09-14 00:55:10,543 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 25 +tpv.core.entities DEBUG 2024-09-14 00:55:10,582 [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=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:55:10,582 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:55:10,588 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:55:10,606 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:55:10,627 [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 2024-09-14 00:55:10,634 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [25] queued (45.834 ms) +galaxy.jobs.handler INFO 2024-09-14 00:55:10,637 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (25) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:55:10,641 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 25 +galaxy.jobs DEBUG 2024-09-14 00:55:10,741 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [25] prepared (80.127 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:55:10,763 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/25/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/25/registry.xml' '/galaxy/server/database/jobs_directory/000/25/upload_params.json' '37:/galaxy/server/database/objects/5/5/f/dataset_55fff3a9-de72-43ff-9f76-a236277f93bd_files:/galaxy/server/database/objects/5/5/f/dataset_55fff3a9-de72-43ff-9f76-a236277f93bd.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:55:10,776 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (25) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/25/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/25/galaxy_25.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:55:15,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 24 finished +galaxy.model.metadata DEBUG 2024-09-14 00:55:15,230 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 36 +galaxy.jobs INFO 2024-09-14 00:55:15,261 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 24 in /galaxy/server/database/jobs_directory/000/24 +galaxy.jobs DEBUG 2024-09-14 00:55:15,304 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 24 executed (105.261 ms) +galaxy.jobs.runners DEBUG 2024-09-14 00:55:18,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 25: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:55:23,242 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 25 finished +galaxy.model.metadata DEBUG 2024-09-14 00:55:23,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 37 +galaxy.jobs INFO 2024-09-14 00:55:23,325 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 25 in /galaxy/server/database/jobs_directory/000/25 +galaxy.jobs DEBUG 2024-09-14 00:55:23,367 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 25 executed (101.237 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:55:23,910 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 26 +tpv.core.entities DEBUG 2024-09-14 00:55:23,943 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/pjbriggs/trimmomatic/trimmomatic/.*, abstract=False, cores=6, mem=12, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[{'name': '_JAVA_OPTIONS', 'value': '-Xmx{int(mem)}G -Xms1G'}], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:55:23,943 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:55:23,947 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:55:23,960 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:55:23,973 [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 2024-09-14 00:55:23,979 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [26] queued (31.853 ms) +galaxy.jobs.handler INFO 2024-09-14 00:55:23,982 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (26) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:55:23,986 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 26 +galaxy.jobs DEBUG 2024-09-14 00:55:24,062 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [26] prepared (58.965 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:55:24,063 [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 2024-09-14 00:55:24,063 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:55:24,081 [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-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:55:24,099 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/26/tool_script.sh] for tool command [if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/5/5/f/dataset_55fff3a9-de72-43ff-9f76-a236277f93bd.dat' fastq_in.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger' fastq_out.'fastqsanger' CROP:10 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger' '/galaxy/server/database/objects/a/7/4/dataset_a742330e-6930-4420-9551-f2011b494d34.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:55:24,109 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:55:24,120 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:55:24,121 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:55:24,136 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:55:29,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 26: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:55:33,472 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 26 finished +galaxy.model.metadata DEBUG 2024-09-14 00:55:33,528 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 38 +galaxy.util WARNING 2024-09-14 00:55:33,534 [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/a/7/4/dataset_a742330e-6930-4420-9551-f2011b494d34.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/a/7/4/dataset_a742330e-6930-4420-9551-f2011b494d34.dat' +galaxy.jobs INFO 2024-09-14 00:55:33,559 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 26 in /galaxy/server/database/jobs_directory/000/26 +galaxy.objectstore CRITICAL 2024-09-14 00:55:33,597 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'tmp8nb3oq1v' +galaxy.jobs DEBUG 2024-09-14 00:55:33,597 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 26 executed (101.026 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:55:36,214 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 27, 28 +tpv.core.entities DEBUG 2024-09-14 00:55:36,247 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:55:36,247 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:55:36,251 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:55:36,265 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:55:36,281 [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 2024-09-14 00:55:36,288 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [27] queued (37.114 ms) +galaxy.jobs.handler INFO 2024-09-14 00:55:36,292 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (27) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:55:36,297 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 27 +tpv.core.entities DEBUG 2024-09-14 00:55:36,308 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:55:36,308 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:55:36,314 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:55:36,330 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:55:36,355 [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 2024-09-14 00:55:36,363 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [28] queued (49.105 ms) +galaxy.jobs.handler INFO 2024-09-14 00:55:36,368 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (28) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:55:36,373 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 28 +galaxy.jobs DEBUG 2024-09-14 00:55:36,405 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [27] prepared (89.437 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:55:36,436 [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' '39:/galaxy/server/database/objects/f/d/6/dataset_fd66c5b9-106d-4919-aced-58fe1b8d5934_files:/galaxy/server/database/objects/f/d/6/dataset_fd66c5b9-106d-4919-aced-58fe1b8d5934.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:55:36,460 [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 $return_code" +galaxy.jobs DEBUG 2024-09-14 00:55:36,481 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [28] prepared (87.720 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:55:36,502 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/28/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/28/registry.xml' '/galaxy/server/database/jobs_directory/000/28/upload_params.json' '40:/galaxy/server/database/objects/d/3/9/dataset_d393355a-1c2b-44f2-8534-fa14c8a5a6c0_files:/galaxy/server/database/objects/d/3/9/dataset_d393355a-1c2b-44f2-8534-fa14c8a5a6c0.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:55:36,514 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (28) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 ERROR 2024-09-14 00:55:45,093 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (28/gxy-ww4c7) User killed running job, but error encountered during termination: Operation cannot be fulfilled on jobs.batch "gxy-ww4c7": the object has been modified; please apply your changes to the latest version and try again +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.108.80.1:443/apis/batch/v1/namespaces/prod-24-09-14-00-32-1/jobs/gxy-ww4c7 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 908, in stop_job + self.__cleanup_k8s_job(k8s_job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-ww4c7": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners DEBUG 2024-09-14 00:55:46,420 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 27: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:55:51,126 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 27 finished +galaxy.model.metadata DEBUG 2024-09-14 00:55:51,187 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 39 +galaxy.jobs INFO 2024-09-14 00:55:51,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 27 in /galaxy/server/database/jobs_directory/000/27 +galaxy.jobs DEBUG 2024-09-14 00:55:51,268 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 27 executed (115.324 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:55:52,670 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 29 +tpv.core.entities DEBUG 2024-09-14 00:55:52,699 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:55:52,700 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:55:52,704 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:55:52,718 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:55:52,732 [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 2024-09-14 00:55:52,738 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [29] queued (34.069 ms) +galaxy.jobs.handler INFO 2024-09-14 00:55:52,741 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (29) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:55:52,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 29 +galaxy.jobs DEBUG 2024-09-14 00:55:52,833 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [29] prepared (70.905 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:55:52,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/29/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/29/registry.xml' '/galaxy/server/database/jobs_directory/000/29/upload_params.json' '41:/galaxy/server/database/objects/9/2/a/dataset_92a08b46-ac6f-476a-8cfa-16e186772b9c_files:/galaxy/server/database/objects/9/2/a/dataset_92a08b46-ac6f-476a-8cfa-16e186772b9c.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:55:52,866 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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.handler DEBUG 2024-09-14 00:55:53,743 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 30 +tpv.core.entities DEBUG 2024-09-14 00:55:53,776 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:55:53,777 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:55:53,781 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:55:53,794 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:55:53,812 [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 2024-09-14 00:55:53,818 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [30] queued (36.791 ms) +galaxy.jobs.handler INFO 2024-09-14 00:55:53,821 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (30) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:55:53,825 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 30 +galaxy.jobs DEBUG 2024-09-14 00:55:53,909 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [30] prepared (67.761 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:55:53,926 [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' '42:/galaxy/server/database/objects/6/c/4/dataset_6c491894-0ad3-4510-a9c4-8a10c6045ac5_files:/galaxy/server/database/objects/6/c/4/dataset_6c491894-0ad3-4510-a9c4-8a10c6045ac5.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:55:53,938 [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 ERROR 2024-09-14 00:56:01,122 [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/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.108.80.1:443/apis/batch/v1/namespaces/prod-24-09-14-00-32-1/jobs/gxy-bh495 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-bh495": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:56:01,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (30/gxy-bh495) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-09-14 00:56:01,165 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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 2024-09-14 00:56:05,688 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 29 finished +galaxy.model.metadata DEBUG 2024-09-14 00:56:05,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 41 +galaxy.jobs INFO 2024-09-14 00:56:05,767 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 29 in /galaxy/server/database/jobs_directory/000/29 +galaxy.jobs DEBUG 2024-09-14 00:56:05,812 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 29 executed (100.949 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:56:08,072 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 31 +tpv.core.entities DEBUG 2024-09-14 00:56:08,100 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:56:08,100 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:56:08,104 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:56:08,116 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:56:08,131 [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 2024-09-14 00:56:08,138 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [31] queued (33.749 ms) +galaxy.jobs.handler INFO 2024-09-14 00:56:08,140 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (31) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:56:08,144 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 31 +galaxy.jobs DEBUG 2024-09-14 00:56:08,238 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [31] prepared (80.240 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:56:08,256 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/31/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/31/registry.xml' '/galaxy/server/database/jobs_directory/000/31/upload_params.json' '43:/galaxy/server/database/objects/8/1/3/dataset_813b5365-28a5-418e-a20e-6b04f7f61870_files:/galaxy/server/database/objects/8/1/3/dataset_813b5365-28a5-418e-a20e-6b04f7f61870.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:56:08,267 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:56:16,419 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 31: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:56:21,085 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 31 finished +galaxy.model.metadata DEBUG 2024-09-14 00:56:21,135 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 43 +galaxy.jobs INFO 2024-09-14 00:56:21,167 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 31 in /galaxy/server/database/jobs_directory/000/31 +galaxy.jobs DEBUG 2024-09-14 00:56:21,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 31 executed (103.062 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:56:22,511 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 32 +tpv.core.entities DEBUG 2024-09-14 00:56:22,543 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/pjbriggs/trimmomatic/trimmomatic/.*, abstract=False, cores=6, mem=12, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[{'name': '_JAVA_OPTIONS', 'value': '-Xmx{int(mem)}G -Xms1G'}], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:56:22,543 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:56:22,548 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:56:22,561 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:56:22,573 [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 2024-09-14 00:56:22,580 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [32] queued (32.014 ms) +galaxy.jobs.handler INFO 2024-09-14 00:56:22,583 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (32) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:56:22,587 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 32 +galaxy.jobs DEBUG 2024-09-14 00:56:22,649 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [32] prepared (46.793 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:56:22,649 [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 2024-09-14 00:56:22,650 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:56:22,666 [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-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:56:22,685 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/32/tool_script.sh] for tool command [if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/8/1/3/dataset_813b5365-28a5-418e-a20e-6b04f7f61870.dat' fastq_in.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger' fastq_out.'fastqsanger' AVGQUAL:30 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger' '/galaxy/server/database/objects/5/5/0/dataset_550be6c4-6a57-46b0-918e-0aacda978dd7.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:56:22,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (32) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/32/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/32/galaxy_32.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:56:22,708 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:56:22,708 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:56:22,723 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:56:27,539 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 32: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:56:32,117 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 32 finished +galaxy.model.metadata DEBUG 2024-09-14 00:56:32,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 44 +galaxy.util WARNING 2024-09-14 00:56:32,182 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/5/5/0/dataset_550be6c4-6a57-46b0-918e-0aacda978dd7.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/5/5/0/dataset_550be6c4-6a57-46b0-918e-0aacda978dd7.dat' +galaxy.jobs INFO 2024-09-14 00:56:32,209 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 32 in /galaxy/server/database/jobs_directory/000/32 +galaxy.objectstore CRITICAL 2024-09-14 00:56:32,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'tmpn3y9yqye' +galaxy.jobs DEBUG 2024-09-14 00:56:32,245 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 32 executed (99.914 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:56:34,820 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 33 +tpv.core.entities DEBUG 2024-09-14 00:56:34,850 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:56:34,851 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:56:34,854 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:56:34,869 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:56:34,883 [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 2024-09-14 00:56:34,889 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [33] queued (34.680 ms) +galaxy.jobs.handler INFO 2024-09-14 00:56:34,892 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (33) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:56:34,897 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 33 +galaxy.jobs DEBUG 2024-09-14 00:56:34,991 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [33] prepared (77.466 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:56:35,011 [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 [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/33/registry.xml' '/galaxy/server/database/jobs_directory/000/33/upload_params.json' '45:/galaxy/server/database/objects/3/7/7/dataset_37778b71-9669-4df5-880b-532f8c4b276b_files:/galaxy/server/database/objects/3/7/7/dataset_37778b71-9669-4df5-880b-532f8c4b276b.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:56:35,023 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:56:42,789 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 33: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:56:47,316 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 33 finished +galaxy.model.metadata DEBUG 2024-09-14 00:56:47,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 45 +galaxy.jobs INFO 2024-09-14 00:56:47,393 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 33 in /galaxy/server/database/jobs_directory/000/33 +galaxy.jobs DEBUG 2024-09-14 00:56:47,437 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 33 executed (98.461 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:56:48,121 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 34 +tpv.core.entities DEBUG 2024-09-14 00:56:48,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/pjbriggs/trimmomatic/trimmomatic/.*, abstract=False, cores=6, mem=12, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[{'name': '_JAVA_OPTIONS', 'value': '-Xmx{int(mem)}G -Xms1G'}], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:56:48,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:56:48,155 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:56:48,166 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:56:48,180 [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 2024-09-14 00:56:48,187 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [34] queued (31.909 ms) +galaxy.jobs.handler INFO 2024-09-14 00:56:48,190 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (34) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:56:48,193 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 34 +galaxy.jobs DEBUG 2024-09-14 00:56:48,252 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [34] prepared (46.499 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:56:48,252 [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 2024-09-14 00:56:48,252 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:56:48,270 [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-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:56:48,290 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/34/tool_script.sh] for tool command [if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/3/7/7/dataset_37778b71-9669-4df5-880b-532f8c4b276b.dat' fastq_in.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger' fastq_out.'fastqsanger' MAXINFO:75:0.8 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger' '/galaxy/server/database/objects/e/6/a/dataset_e6ac6186-9f77-45ca-a14f-43c8894a7811.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:56:48,299 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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.tool_util.deps.containers INFO 2024-09-14 00:56:48,310 [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 2024-09-14 00:56:48,310 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:56:48,326 [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-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.runners.kubernetes ERROR 2024-09-14 00:56:51,996 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (34/gxy-q74tk) User killed running job, but error encountered during termination: Operation cannot be fulfilled on jobs.batch "gxy-q74tk": the object has been modified; please apply your changes to the latest version and try again +Traceback (most recent call last): + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.108.80.1:443/apis/batch/v1/namespaces/prod-24-09-14-00-32-1/jobs/gxy-q74tk + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 908, in stop_job + self.__cleanup_k8s_job(k8s_job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-q74tk": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes ERROR 2024-09-14 00:56:52,006 [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/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.108.80.1:443/apis/batch/v1/namespaces/prod-24-09-14-00-32-1/jobs/gxy-q74tk + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-q74tk": the object has been modified; please apply your changes to the latest version and try again +galaxy.util WARNING 2024-09-14 00:56:52,052 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/6/a/dataset_e6ac6186-9f77-45ca-a14f-43c8894a7811.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/6/a/dataset_e6ac6186-9f77-45ca-a14f-43c8894a7811.dat' +galaxy.objectstore CRITICAL 2024-09-14 00:56:52,071 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmpzel01lhj' +galaxy.jobs.handler DEBUG 2024-09-14 00:56:54,289 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 35, 36 +tpv.core.entities DEBUG 2024-09-14 00:56:54,318 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:56:54,318 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:56:54,322 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:56:54,335 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:56:54,349 [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 2024-09-14 00:56:54,354 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [35] queued (31.904 ms) +galaxy.jobs.handler INFO 2024-09-14 00:56:54,357 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (35) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:56:54,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 35 +tpv.core.entities DEBUG 2024-09-14 00:56:54,370 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:56:54,371 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:56:54,376 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:56:54,391 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:56:54,415 [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 2024-09-14 00:56:54,422 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [36] queued (45.665 ms) +galaxy.jobs.handler INFO 2024-09-14 00:56:54,425 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (36) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:56:54,429 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 36 +galaxy.jobs DEBUG 2024-09-14 00:56:54,468 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [35] prepared (86.077 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:56:54,492 [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 [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/35/registry.xml' '/galaxy/server/database/jobs_directory/000/35/upload_params.json' '47:/galaxy/server/database/objects/b/7/4/dataset_b74d1d24-cc83-446c-8e1b-fb992fd7d3d0_files:/galaxy/server/database/objects/b/7/4/dataset_b74d1d24-cc83-446c-8e1b-fb992fd7d3d0.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:56:54,512 [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 $return_code" +galaxy.jobs DEBUG 2024-09-14 00:56:54,533 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [36] prepared (86.807 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:56:54,553 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/36/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/36/registry.xml' '/galaxy/server/database/jobs_directory/000/36/upload_params.json' '48:/galaxy/server/database/objects/b/b/a/dataset_bba28ac0-b3cc-4554-aad7-1a22ba1bf5f1_files:/galaxy/server/database/objects/b/b/a/dataset_bba28ac0-b3cc-4554-aad7-1a22ba1bf5f1.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:56:54,563 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (36) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:57:02,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 35: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:57:02,595 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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 2024-09-14 00:57:07,143 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 36 finished +galaxy.model.metadata DEBUG 2024-09-14 00:57:07,193 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 48 +galaxy.jobs INFO 2024-09-14 00:57:07,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 36 in /galaxy/server/database/jobs_directory/000/36 +galaxy.jobs.runners DEBUG 2024-09-14 00:57:07,231 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 35 finished +galaxy.jobs DEBUG 2024-09-14 00:57:07,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 36 executed (107.143 ms) +galaxy.model.metadata DEBUG 2024-09-14 00:57:07,278 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 47 +galaxy.jobs INFO 2024-09-14 00:57:07,309 [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 2024-09-14 00:57:07,353 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 35 executed (102.068 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:57:08,803 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 37 +tpv.core.entities DEBUG 2024-09-14 00:57:08,838 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/pjbriggs/trimmomatic/trimmomatic/.*, abstract=False, cores=6, mem=12, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[{'name': '_JAVA_OPTIONS', 'value': '-Xmx{int(mem)}G -Xms1G'}], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:57:08,839 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:57:08,843 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:57:08,855 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:57:08,875 [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 2024-09-14 00:57:08,882 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [37] queued (38.983 ms) +galaxy.jobs.handler INFO 2024-09-14 00:57:08,885 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (37) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:57:08,889 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 37 +galaxy.jobs DEBUG 2024-09-14 00:57:08,971 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [37] prepared (68.029 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:57:08,971 [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 2024-09-14 00:57:08,971 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:57:08,989 [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-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:57:09,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/37/tool_script.sh] for tool command [if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/b/7/4/dataset_b74d1d24-cc83-446c-8e1b-fb992fd7d3d0.dat' fastq_r1.'fastqsanger' && ln -s '/galaxy/server/database/objects/b/b/a/dataset_bba28ac0-b3cc-4554-aad7-1a22ba1bf5f1.dat' fastq_r2.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar PE -threads ${GALAXY_SLOTS:-6} fastq_r1.'fastqsanger' fastq_r2.'fastqsanger' fastq_out_r1_paired.'fastqsanger' fastq_out_r1_unpaired.'fastqsanger' fastq_out_r2_paired.'fastqsanger' fastq_out_r2_unpaired.'fastqsanger' ILLUMINACLIP:$TRIMMOMATIC_ADAPTERS_PATH/TruSeq2-PE.fa:2:30:10:8:true SLIDINGWINDOW:4:20 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out_r1_paired.'fastqsanger' '/galaxy/server/database/objects/e/b/e/dataset_ebefc30b-64a9-4eaa-8ad4-90b220b8f810.dat' && mv fastq_out_r1_unpaired.'fastqsanger' '/galaxy/server/database/objects/2/e/d/dataset_2ed584e0-3edb-42f1-98d7-76aefc7d8ce4.dat' && mv fastq_out_r2_paired.'fastqsanger' '/galaxy/server/database/objects/2/b/1/dataset_2b19ddb7-e787-4a65-83db-984b32389de8.dat' && mv fastq_out_r2_unpaired.'fastqsanger' '/galaxy/server/database/objects/3/4/7/dataset_34763ef0-a6f1-4296-a0fd-a1380ef45a17.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:57:09,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (37) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:57:09,049 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:57:09,049 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:57:09,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:57:13,778 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 37: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:57:18,404 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 37 finished +galaxy.model.metadata DEBUG 2024-09-14 00:57:18,455 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 49 +galaxy.model.metadata DEBUG 2024-09-14 00:57:18,463 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 50 +galaxy.model.metadata DEBUG 2024-09-14 00:57:18,492 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 51 +galaxy.model.metadata DEBUG 2024-09-14 00:57:18,524 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 52 +galaxy.util WARNING 2024-09-14 00:57:18,530 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/b/e/dataset_ebefc30b-64a9-4eaa-8ad4-90b220b8f810.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/b/e/dataset_ebefc30b-64a9-4eaa-8ad4-90b220b8f810.dat' +galaxy.util WARNING 2024-09-14 00:57:18,531 [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/2/b/1/dataset_2b19ddb7-e787-4a65-83db-984b32389de8.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/1/dataset_2b19ddb7-e787-4a65-83db-984b32389de8.dat' +galaxy.util WARNING 2024-09-14 00:57:18,531 [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/2/e/d/dataset_2ed584e0-3edb-42f1-98d7-76aefc7d8ce4.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/e/d/dataset_2ed584e0-3edb-42f1-98d7-76aefc7d8ce4.dat' +galaxy.util WARNING 2024-09-14 00:57:18,531 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/3/4/7/dataset_34763ef0-a6f1-4296-a0fd-a1380ef45a17.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/3/4/7/dataset_34763ef0-a6f1-4296-a0fd-a1380ef45a17.dat' +galaxy.jobs INFO 2024-09-14 00:57:18,559 [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.objectstore CRITICAL 2024-09-14 00:57:18,602 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'tmpmpm8iwu4' +galaxy.jobs DEBUG 2024-09-14 00:57:18,603 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 37 executed (174.172 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:57:23,151 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 38 +tpv.core.entities DEBUG 2024-09-14 00:57:23,178 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:57:23,178 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:57:23,182 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:57:23,194 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:57:23,207 [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 2024-09-14 00:57:23,213 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [38] queued (30.730 ms) +galaxy.jobs.handler INFO 2024-09-14 00:57:23,215 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (38) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:57:23,218 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 38 +galaxy.jobs DEBUG 2024-09-14 00:57:23,297 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [38] prepared (66.224 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:57:23,316 [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' '53:/galaxy/server/database/objects/b/a/c/dataset_bacff905-1aea-4550-8e00-06b2da9d0d44_files:/galaxy/server/database/objects/b/a/c/dataset_bacff905-1aea-4550-8e00-06b2da9d0d44.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:57:23,325 [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.handler DEBUG 2024-09-14 00:57:24,218 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 39 +tpv.core.entities DEBUG 2024-09-14 00:57:24,246 [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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:57:24,247 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:57:24,250 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:57:24,263 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:57:24,279 [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 2024-09-14 00:57:24,286 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [39] queued (35.150 ms) +galaxy.jobs.handler INFO 2024-09-14 00:57:24,291 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (39) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:57:24,292 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 39 +galaxy.jobs DEBUG 2024-09-14 00:57:24,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [39] prepared (70.924 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:57:24,397 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/39/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/39/registry.xml' '/galaxy/server/database/jobs_directory/000/39/upload_params.json' '54:/galaxy/server/database/objects/7/c/4/dataset_7c4914e7-e63d-4a57-ba43-c56a3c9e5b9e_files:/galaxy/server/database/objects/7/c/4/dataset_7c4914e7-e63d-4a57-ba43-c56a3c9e5b9e.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:57:24,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (39) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/39/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/39/galaxy_39.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:57:31,112 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 38: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:57:32,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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 2024-09-14 00:57:35,924 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 38 finished +galaxy.model.metadata DEBUG 2024-09-14 00:57:35,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 53 +galaxy.jobs INFO 2024-09-14 00:57:36,006 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 38 in /galaxy/server/database/jobs_directory/000/38 +galaxy.jobs DEBUG 2024-09-14 00:57:36,050 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 38 executed (102.255 ms) +galaxy.jobs.runners DEBUG 2024-09-14 00:57:36,810 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 39 finished +galaxy.model.metadata DEBUG 2024-09-14 00:57:36,868 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 54 +galaxy.jobs INFO 2024-09-14 00:57:36,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 39 in /galaxy/server/database/jobs_directory/000/39 +galaxy.jobs DEBUG 2024-09-14 00:57:36,957 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 39 executed (120.896 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:57:37,542 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 40 +tpv.core.entities DEBUG 2024-09-14 00:57:37,576 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/pjbriggs/trimmomatic/trimmomatic/.*, abstract=False, cores=6, mem=12, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[{'name': '_JAVA_OPTIONS', 'value': '-Xmx{int(mem)}G -Xms1G'}], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:57:37,576 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:57:37,581 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:57:37,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:57:37,622 [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 2024-09-14 00:57:37,630 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [40] queued (48.931 ms) +galaxy.jobs.handler INFO 2024-09-14 00:57:37,634 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (40) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:57:37,638 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 40 +galaxy.jobs DEBUG 2024-09-14 00:57:37,725 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [40] prepared (72.628 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:57:37,725 [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 2024-09-14 00:57:37,725 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:57:37,744 [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-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:57:37,764 [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 [if [ -z "$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z "$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/b/a/c/dataset_bacff905-1aea-4550-8e00-06b2da9d0d44.dat' fastq_r1.'fastqsanger' && ln -s '/galaxy/server/database/objects/7/c/4/dataset_7c4914e7-e63d-4a57-ba43-c56a3c9e5b9e.dat' fastq_r2.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar PE -threads ${GALAXY_SLOTS:-6} fastq_r1.'fastqsanger' fastq_r2.'fastqsanger' fastq_out_r1_paired.'fastqsanger' fastq_out_r1_unpaired.'fastqsanger' fastq_out_r2_paired.'fastqsanger' fastq_out_r2_unpaired.'fastqsanger' ILLUMINACLIP:/galaxy/server/database/jobs_directory/000/40/configs/tmpt_pbf1wi:2:30:10:8:true SLIDINGWINDOW:4:20 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out_r1_paired.'fastqsanger' '/galaxy/server/database/objects/6/8/d/dataset_68d481dc-c54b-4615-9c9d-b2fbf44c03e1.dat' && mv fastq_out_r1_unpaired.'fastqsanger' '/galaxy/server/database/objects/b/a/6/dataset_ba65a7a6-dd02-4d71-a498-457c47b73d4c.dat' && mv fastq_out_r2_paired.'fastqsanger' '/galaxy/server/database/objects/e/a/2/dataset_ea23499c-9ddf-4ab5-b3af-d7aca44fca60.dat' && mv fastq_out_r2_unpaired.'fastqsanger' '/galaxy/server/database/objects/c/e/0/dataset_ce021ec2-5f0a-4305-92d1-88a7fb78e9c4.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:57:37,797 [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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:57:37,808 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:57:37,808 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1: mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e +galaxy.tool_util.deps.containers INFO 2024-09-14 00:57:37,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-e1a6ade46756da3bd8ceef31e6d2e7645f383a87:5cea15127895d50e80d4a0350938adabaf77375e-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:57:42,520 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 40: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:57:47,148 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 40 finished +galaxy.model.metadata DEBUG 2024-09-14 00:57:47,205 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 55 +galaxy.model.metadata DEBUG 2024-09-14 00:57:47,213 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 56 +galaxy.model.metadata DEBUG 2024-09-14 00:57:47,242 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 57 +galaxy.model.metadata DEBUG 2024-09-14 00:57:47,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 58 +galaxy.util WARNING 2024-09-14 00:57:47,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/6/8/d/dataset_68d481dc-c54b-4615-9c9d-b2fbf44c03e1.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/6/8/d/dataset_68d481dc-c54b-4615-9c9d-b2fbf44c03e1.dat' +galaxy.util WARNING 2024-09-14 00:57:47,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/a/2/dataset_ea23499c-9ddf-4ab5-b3af-d7aca44fca60.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/a/2/dataset_ea23499c-9ddf-4ab5-b3af-d7aca44fca60.dat' +galaxy.util WARNING 2024-09-14 00:57:47,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/b/a/6/dataset_ba65a7a6-dd02-4d71-a498-457c47b73d4c.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/b/a/6/dataset_ba65a7a6-dd02-4d71-a498-457c47b73d4c.dat' +galaxy.util WARNING 2024-09-14 00:57:47,284 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/c/e/0/dataset_ce021ec2-5f0a-4305-92d1-88a7fb78e9c4.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/c/e/0/dataset_ce021ec2-5f0a-4305-92d1-88a7fb78e9c4.dat' +galaxy.jobs INFO 2024-09-14 00:57:47,315 [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.objectstore CRITICAL 2024-09-14 00:57:47,362 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'tmpt_pbf1wi' +galaxy.jobs DEBUG 2024-09-14 00:57:47,363 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 40 executed (186.256 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:57:53,946 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 41 +tpv.core.entities DEBUG 2024-09-14 00:57:53,972 [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=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:57:53,973 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:57:53,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:57:53,989 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:57:54,001 [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 2024-09-14 00:57:54,007 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [41] queued (29.513 ms) +galaxy.jobs.handler INFO 2024-09-14 00:57:54,011 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (41) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:57:54,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 41 +galaxy.jobs DEBUG 2024-09-14 00:57:54,100 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [41] prepared (71.717 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:57:54,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/41/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/41/registry.xml' '/galaxy/server/database/jobs_directory/000/41/upload_params.json' '59:/galaxy/server/database/objects/f/5/e/dataset_f5e427bb-e571-42d6-8da6-083fa7944e3c_files:/galaxy/server/database/objects/f/5/e/dataset_f5e427bb-e571-42d6-8da6-083fa7944e3c.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:57:54,129 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (41) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/41/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/41/galaxy_41.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:58:02,697 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 41: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:58:07,479 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 41 finished +galaxy.model.metadata DEBUG 2024-09-14 00:58:07,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 59 +galaxy.jobs INFO 2024-09-14 00:58:07,579 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 41 in /galaxy/server/database/jobs_directory/000/41 +galaxy.jobs DEBUG 2024-09-14 00:58:07,636 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 41 executed (128.981 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:58:08,289 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 42 +tpv.core.entities DEBUG 2024-09-14 00:58:08,326 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:58:08,326 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:58:08,331 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:58:08,347 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:58:08,367 [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 2024-09-14 00:58:08,378 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [42] queued (47.355 ms) +galaxy.jobs.handler INFO 2024-09-14 00:58:08,382 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (42) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:58:08,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 42 +galaxy.tools.wrappers WARNING 2024-09-14 00:58:08,448 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Datatype class not found for extension 'qnamed_input_sorted.bam', which is used as parameter of 'is_of_type()' method +galaxy.jobs DEBUG 2024-09-14 00:58:08,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [42] prepared (57.752 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:58:08,463 [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 2024-09-14 00:58:08,463 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-14 00:58:08,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:58:08,717 [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 [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/42/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -n -O BAM -o namesorted.bam '/galaxy/server/database/objects/f/5/e/dataset_f5e427bb-e571-42d6-8da6-083fa7944e3c.dat' && samtools fixmate -@ $addthreads -O BAM namesorted.bam '/galaxy/server/database/objects/c/6/4/dataset_c64cf9bf-5bb1-441a-9725-9f06ed3224f4.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:58:08,730 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (42) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:58:08,742 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:58:08,742 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-14 00:58:08,762 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:58:15,858 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 42: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:58:20,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 42 finished +galaxy.model.metadata DEBUG 2024-09-14 00:58:20,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 60 +galaxy.jobs INFO 2024-09-14 00:58:20,679 [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 2024-09-14 00:58:20,720 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 42 executed (114.438 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:58:23,708 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 43 +tpv.core.entities DEBUG 2024-09-14 00:58:23,741 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:58:23,742 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:58:23,747 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:58:23,762 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:58:23,780 [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 2024-09-14 00:58:23,787 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [43] queued (40.296 ms) +galaxy.jobs.handler INFO 2024-09-14 00:58:23,791 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (43) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:58:23,796 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 43 +galaxy.jobs DEBUG 2024-09-14 00:58:23,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [43] prepared (87.005 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:58:23,921 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/43/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/43/registry.xml' '/galaxy/server/database/jobs_directory/000/43/upload_params.json' '61:/galaxy/server/database/objects/2/f/6/dataset_2f6e9d6b-dde5-40e8-88d9-205956152cfe_files:/galaxy/server/database/objects/2/f/6/dataset_2f6e9d6b-dde5-40e8-88d9-205956152cfe.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:58:23,934 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:58:33,149 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 43: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:58:37,630 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 43 finished +galaxy.model.metadata DEBUG 2024-09-14 00:58:37,681 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 61 +galaxy.jobs INFO 2024-09-14 00:58:37,718 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 43 in /galaxy/server/database/jobs_directory/000/43 +galaxy.jobs DEBUG 2024-09-14 00:58:37,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 43 executed (112.290 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:58:38,185 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 44 +tpv.core.entities DEBUG 2024-09-14 00:58:38,219 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:58:38,220 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:58:38,225 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:58:38,240 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:58:38,257 [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 2024-09-14 00:58:38,263 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [44] queued (38.374 ms) +galaxy.jobs.handler INFO 2024-09-14 00:58:38,269 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (44) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:58:38,270 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 44 +galaxy.tools.wrappers WARNING 2024-09-14 00:58:38,318 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Datatype class not found for extension 'qnamed_input_sorted.bam', which is used as parameter of 'is_of_type()' method +galaxy.jobs DEBUG 2024-09-14 00:58:38,332 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [44] prepared (47.474 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:58:38,333 [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 2024-09-14 00:58:38,333 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-14 00:58:38,354 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:58:38,378 [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 [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/44/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -n -O BAM -o namesorted.bam '/galaxy/server/database/objects/2/f/6/dataset_2f6e9d6b-dde5-40e8-88d9-205956152cfe.dat' && samtools fixmate -@ $addthreads -O BAM namesorted.bam '/galaxy/server/database/objects/6/b/f/dataset_6bf48682-2492-427b-a543-91dc947a9fd4.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:58:38,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (44) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:58:38,398 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:58:38,398 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-14 00:58:38,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:58:43,336 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 44: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:58:47,867 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 44 finished +galaxy.model.metadata DEBUG 2024-09-14 00:58:47,918 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 62 +galaxy.jobs INFO 2024-09-14 00:58:47,946 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 44 in /galaxy/server/database/jobs_directory/000/44 +galaxy.jobs DEBUG 2024-09-14 00:58:47,983 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 44 executed (93.866 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:58:50,494 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 45 +tpv.core.entities DEBUG 2024-09-14 00:58:50,522 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:58:50,522 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:58:50,526 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:58:50,539 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:58:50,554 [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 2024-09-14 00:58:50,560 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [45] queued (34.274 ms) +galaxy.jobs.handler INFO 2024-09-14 00:58:50,563 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (45) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:58:50,568 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 45 +galaxy.jobs DEBUG 2024-09-14 00:58:50,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [45] prepared (77.391 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:58:50,679 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/45/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/45/registry.xml' '/galaxy/server/database/jobs_directory/000/45/upload_params.json' '63:/galaxy/server/database/objects/b/e/9/dataset_be99792b-bc31-436a-a99b-041baf3e87a0_files:/galaxy/server/database/objects/b/e/9/dataset_be99792b-bc31-436a-a99b-041baf3e87a0.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:58:50,690 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:58:58,601 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 45: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:59:03,372 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 45 finished +galaxy.model.metadata DEBUG 2024-09-14 00:59:03,424 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 63 +galaxy.jobs INFO 2024-09-14 00:59:03,460 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 45 in /galaxy/server/database/jobs_directory/000/45 +galaxy.jobs DEBUG 2024-09-14 00:59:03,505 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 45 executed (107.167 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:59:04,846 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 46 +tpv.core.entities DEBUG 2024-09-14 00:59:04,881 [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=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:59:04,882 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:59:04,887 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:59:04,902 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:59:04,919 [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 2024-09-14 00:59:04,927 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [46] queued (39.912 ms) +galaxy.jobs.handler INFO 2024-09-14 00:59:04,930 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (46) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:59:04,935 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 46 +galaxy.tools.wrappers WARNING 2024-09-14 00:59:05,002 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Datatype class not found for extension 'qnamed_input_sorted.bam', which is used as parameter of 'is_of_type()' method +galaxy.jobs DEBUG 2024-09-14 00:59:05,016 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [46] prepared (59.382 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:59:05,017 [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 2024-09-14 00:59:05,017 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-14 00:59:05,039 [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 2024-09-14 00:59:05,062 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/46/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/46/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -n -O BAM -o namesorted.bam '/galaxy/server/database/objects/b/e/9/dataset_be99792b-bc31-436a-a99b-041baf3e87a0.dat' && samtools fixmate -@ $addthreads -O BAM namesorted.bam '/galaxy/server/database/objects/c/e/b/dataset_cebc47f5-0560-4b13-91ed-921a1c4978a1.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:59:05,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (46) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:59:05,085 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:59:05,085 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-14 00:59:05,104 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:59:09,732 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 46: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 00:59:14,320 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 46 finished +galaxy.model.metadata DEBUG 2024-09-14 00:59:14,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 64 +galaxy.jobs INFO 2024-09-14 00:59:14,410 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 46 in /galaxy/server/database/jobs_directory/000/46 +galaxy.jobs DEBUG 2024-09-14 00:59:14,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 46 executed (108.580 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:59:17,182 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 47 +tpv.core.entities DEBUG 2024-09-14 00:59:17,217 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:59:17,217 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:59:17,222 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:59:17,237 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:59:17,257 [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 2024-09-14 00:59:17,263 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [47] queued (41.276 ms) +galaxy.jobs.handler INFO 2024-09-14 00:59:17,267 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (47) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:59:17,271 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 47 +galaxy.jobs DEBUG 2024-09-14 00:59:17,370 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [47] prepared (80.387 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:59:17,390 [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 [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/47/registry.xml' '/galaxy/server/database/jobs_directory/000/47/upload_params.json' '65:/galaxy/server/database/objects/5/b/0/dataset_5b0b2b6f-2579-4163-aeb1-f92910b538c1_files:/galaxy/server/database/objects/5/b/0/dataset_5b0b2b6f-2579-4163-aeb1-f92910b538c1.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:59:17,400 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:59:25,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 47: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:59:30,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 47 finished +galaxy.model.metadata DEBUG 2024-09-14 00:59:30,647 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 65 +galaxy.jobs INFO 2024-09-14 00:59:30,678 [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 2024-09-14 00:59:30,715 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 47 executed (92.029 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:59:31,530 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 48 +tpv.core.entities DEBUG 2024-09-14 00:59:31,562 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:59:31,562 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:59:31,567 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:59:31,580 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:59:31,595 [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 2024-09-14 00:59:31,602 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [48] queued (34.994 ms) +galaxy.jobs.handler INFO 2024-09-14 00:59:31,605 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (48) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:59:31,609 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 48 +galaxy.tools.wrappers WARNING 2024-09-14 00:59:31,664 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Datatype class not found for extension 'qnamed_input_sorted.bam', which is used as parameter of 'is_of_type()' method +galaxy.jobs DEBUG 2024-09-14 00:59:31,676 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [48] prepared (49.527 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:59:31,676 [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 2024-09-14 00:59:31,677 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-14 00:59:31,897 [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 2024-09-14 00:59:31,918 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/48/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/48/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -n -O BAM -o namesorted.bam '/galaxy/server/database/objects/5/b/0/dataset_5b0b2b6f-2579-4163-aeb1-f92910b538c1.dat' && samtools fixmate -@ $addthreads -c -O BAM namesorted.bam '/galaxy/server/database/objects/5/3/2/dataset_53232fba-fa44-4e74-b45a-c8ffe4212f3b.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:59:31,929 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (48) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/48/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/48/galaxy_48.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:59:31,942 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:59:31,942 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-14 00:59:31,960 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 00:59:36,039 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 48: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:59:40,661 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 48 finished +galaxy.model.metadata DEBUG 2024-09-14 00:59:40,714 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 66 +galaxy.jobs INFO 2024-09-14 00:59:40,740 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 48 in /galaxy/server/database/jobs_directory/000/48 +galaxy.jobs DEBUG 2024-09-14 00:59:40,789 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 48 executed (101.614 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:59:42,821 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 49 +tpv.core.entities DEBUG 2024-09-14 00:59:42,853 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:59:42,853 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:59:42,860 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:59:42,874 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:59:42,887 [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 2024-09-14 00:59:42,892 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [49] queued (32.422 ms) +galaxy.jobs.handler INFO 2024-09-14 00:59:42,895 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (49) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:59:42,898 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 49 +galaxy.jobs DEBUG 2024-09-14 00:59:42,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [49] prepared (74.164 ms) +galaxy.jobs.command_factory INFO 2024-09-14 00:59:43,007 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/49/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/49/registry.xml' '/galaxy/server/database/jobs_directory/000/49/upload_params.json' '67:/galaxy/server/database/objects/8/6/a/dataset_86af6636-b6a5-414c-abe9-d126745b097d_files:/galaxy/server/database/objects/8/6/a/dataset_86af6636-b6a5-414c-abe9-d126745b097d.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:59:43,019 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (49) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/49/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/49/galaxy_49.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 00:59:51,328 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 49: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 00:59:55,853 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 49 finished +galaxy.model.metadata DEBUG 2024-09-14 00:59:55,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 67 +galaxy.jobs INFO 2024-09-14 00:59:55,939 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 49 in /galaxy/server/database/jobs_directory/000/49 +galaxy.jobs DEBUG 2024-09-14 00:59:55,982 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 49 executed (102.709 ms) +galaxy.jobs.handler DEBUG 2024-09-14 00:59:57,171 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 50 +tpv.core.entities DEBUG 2024-09-14 00:59:57,202 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 00:59:57,202 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 00:59:57,207 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 00:59:57,220 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 00:59:57,235 [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 2024-09-14 00:59:57,242 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [50] queued (34.610 ms) +galaxy.jobs.handler INFO 2024-09-14 00:59:57,245 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (50) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 00:59:57,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 50 +galaxy.tools.wrappers WARNING 2024-09-14 00:59:57,309 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Datatype class not found for extension 'qnamed_input_sorted.bam', which is used as parameter of 'is_of_type()' method +galaxy.jobs DEBUG 2024-09-14 00:59:57,321 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [50] prepared (54.995 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 00:59:57,322 [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 2024-09-14 00:59:57,322 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-14 00:59:57,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 00:59:57,363 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/50/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/50/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -n -O BAM -o namesorted.bam '/galaxy/server/database/objects/8/6/a/dataset_86af6636-b6a5-414c-abe9-d126745b097d.dat' && samtools fixmate -@ $addthreads -c -O BAM namesorted.bam '/galaxy/server/database/objects/b/d/0/dataset_bd0e801d-4044-4546-8ed4-0b3a50ed5ea8.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 00:59:57,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (50) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/50/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/50/galaxy_50.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 00:59:57,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 00:59:57,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-14 00:59:57,404 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:00:01,814 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 50: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:00:06,416 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 50 finished +galaxy.model.metadata DEBUG 2024-09-14 01:00:06,477 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 68 +galaxy.jobs INFO 2024-09-14 01:00:06,507 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 50 in /galaxy/server/database/jobs_directory/000/50 +galaxy.jobs DEBUG 2024-09-14 01:00:06,550 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 50 executed (99.613 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:00:08,466 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 51 +tpv.core.entities DEBUG 2024-09-14 01:00:08,503 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:00:08,504 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:00:08,509 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:00:08,526 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:00:08,544 [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 2024-09-14 01:00:08,551 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [51] queued (42.424 ms) +galaxy.jobs.handler INFO 2024-09-14 01:00:08,555 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (51) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:00:08,559 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 51 +galaxy.jobs DEBUG 2024-09-14 01:00:08,654 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [51] prepared (77.242 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:00:08,673 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/51/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/51/registry.xml' '/galaxy/server/database/jobs_directory/000/51/upload_params.json' '69:/galaxy/server/database/objects/a/c/c/dataset_acc0c902-0bf8-48c1-8798-2700ee364ab7_files:/galaxy/server/database/objects/a/c/c/dataset_acc0c902-0bf8-48c1-8798-2700ee364ab7.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:00:08,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:00:17,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 51: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:00:21,667 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 51 finished +galaxy.model.metadata DEBUG 2024-09-14 01:00:21,713 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 69 +galaxy.jobs INFO 2024-09-14 01:00:21,744 [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 2024-09-14 01:00:21,785 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 51 executed (93.888 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:00:22,869 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 52 +tpv.core.entities DEBUG 2024-09-14 01:00:22,901 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:00:22,902 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:00:22,906 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:00:22,919 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:00:22,934 [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 2024-09-14 01:00:22,941 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [52] queued (34.460 ms) +galaxy.jobs.handler INFO 2024-09-14 01:00:22,944 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (52) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:00:22,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 52 +galaxy.tools.wrappers WARNING 2024-09-14 01:00:22,998 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Datatype class not found for extension 'qnamed_input_sorted.bam', which is used as parameter of 'is_of_type()' method +galaxy.jobs DEBUG 2024-09-14 01:00:23,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [52] prepared (46.995 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:00:23,010 [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 2024-09-14 01:00:23,010 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:00:23,031 [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 2024-09-14 01:00:23,051 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/52/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/52/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -n -O BAM -o namesorted.bam '/galaxy/server/database/objects/a/c/c/dataset_acc0c902-0bf8-48c1-8798-2700ee364ab7.dat' && samtools fixmate -@ $addthreads -O BAM namesorted.bam '/galaxy/server/database/objects/f/5/9/dataset_f59012cb-1c29-4dbd-b749-baeaba5e6402.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:00:23,064 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (52) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/52/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/52/galaxy_52.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:00:23,075 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:00:23,075 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9: samtools:1.9 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:00:23,095 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.9--h10a08f8_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:00:27,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 52: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:00:31,740 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 52 finished +galaxy.model.metadata DEBUG 2024-09-14 01:00:31,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 70 +galaxy.jobs INFO 2024-09-14 01:00:31,817 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 52 in /galaxy/server/database/jobs_directory/000/52 +galaxy.jobs DEBUG 2024-09-14 01:00:31,856 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 52 executed (91.162 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:00:35,335 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 53 +tpv.core.entities DEBUG 2024-09-14 01:00:35,365 [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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:00:35,366 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:00:35,370 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:00:35,384 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:00:35,398 [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 2024-09-14 01:00:35,404 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [53] queued (33.747 ms) +galaxy.jobs.handler INFO 2024-09-14 01:00:35,407 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (53) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:00:35,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 53 +galaxy.jobs DEBUG 2024-09-14 01:00:35,503 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [53] prepared (75.783 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:00:35,523 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/53/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/53/registry.xml' '/galaxy/server/database/jobs_directory/000/53/upload_params.json' '71:/galaxy/server/database/objects/f/3/7/dataset_f37973fd-efc1-49f4-bca4-2083b7e3bc47_files:/galaxy/server/database/objects/f/3/7/dataset_f37973fd-efc1-49f4-bca4-2083b7e3bc47.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:00:35,534 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (53) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/53/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/53/galaxy_53.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-09-14 01:00:36,409 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 54 +tpv.core.entities DEBUG 2024-09-14 01:00:36,437 [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=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:00:36,438 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:00:36,442 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:00:36,455 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:00:36,470 [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 2024-09-14 01:00:36,476 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [54] queued (33.837 ms) +galaxy.jobs.handler INFO 2024-09-14 01:00:36,479 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (54) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:00:36,482 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 54 +galaxy.jobs DEBUG 2024-09-14 01:00:36,563 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [54] prepared (66.300 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:00:36,580 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '72:/galaxy/server/database/objects/c/d/3/dataset_cd37bd50-8ef0-44f6-9550-06b20e271e97_files:/galaxy/server/database/objects/c/d/3/dataset_cd37bd50-8ef0-44f6-9550-06b20e271e97.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:00:36,590 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 ERROR 2024-09-14 01:00:42,534 [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/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.108.80.1:443/apis/batch/v1/namespaces/prod-24-09-14-00-32-1/jobs/gxy-hp87m + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-hp87m": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:00:42,588 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (53/gxy-hp87m) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-09-14 01:00:44,626 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 56, 55 +tpv.core.entities DEBUG 2024-09-14 01:00:44,654 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:00:44,654 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:00:44,658 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:00:44,673 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:00:44,688 [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 2024-09-14 01:00:44,694 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [55] queued (36.196 ms) +galaxy.jobs.handler INFO 2024-09-14 01:00:44,700 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (55) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:00:44,704 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 55 +tpv.core.entities DEBUG 2024-09-14 01:00:44,713 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:00:44,713 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:00:44,718 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:00:44,731 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:00:44,753 [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 2024-09-14 01:00:44,758 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [56] queued (40.160 ms) +galaxy.jobs.handler INFO 2024-09-14 01:00:44,765 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (56) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:00:44,768 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 56 +galaxy.jobs DEBUG 2024-09-14 01:00:44,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [55] prepared (95.839 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:00:44,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/55/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/55/registry.xml' '/galaxy/server/database/jobs_directory/000/55/upload_params.json' '73:/galaxy/server/database/objects/4/c/3/dataset_4c33dcfc-06db-4200-9078-534cadb9f3e5_files:/galaxy/server/database/objects/4/c/3/dataset_4c33dcfc-06db-4200-9078-534cadb9f3e5.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:00:44,854 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (55) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/55/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/55/galaxy_55.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-09-14 01:00:44,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [56] prepared (85.660 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:00:44,892 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/56/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/56/registry.xml' '/galaxy/server/database/jobs_directory/000/56/upload_params.json' '74:/galaxy/server/database/objects/4/1/c/dataset_41c32e09-608f-4ddf-85e2-13bea3229eb4_files:/galaxy/server/database/objects/4/1/c/dataset_41c32e09-608f-4ddf-85e2-13bea3229eb4.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:00:44,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (56) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 ERROR 2024-09-14 01:00:44,934 [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/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.108.80.1:443/apis/batch/v1/namespaces/prod-24-09-14-00-32-1/jobs/gxy-xpxbv + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-xpxbv": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:00:45,365 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (54/gxy-xpxbv) Terminated at user's request +galaxy.jobs.runners DEBUG 2024-09-14 01:00:53,372 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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 2024-09-14 01:00:53,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 56: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:00:58,116 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 56 finished +galaxy.model.metadata DEBUG 2024-09-14 01:00:58,166 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 74 +galaxy.jobs.runners DEBUG 2024-09-14 01:00:58,198 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 55 finished +galaxy.jobs INFO 2024-09-14 01:00:58,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 56 in /galaxy/server/database/jobs_directory/000/56 +galaxy.model.metadata DEBUG 2024-09-14 01:00:58,251 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 73 +galaxy.jobs DEBUG 2024-09-14 01:00:58,258 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 56 executed (117.131 ms) +galaxy.jobs INFO 2024-09-14 01:00:58,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 55 in /galaxy/server/database/jobs_directory/000/55 +galaxy.jobs DEBUG 2024-09-14 01:00:58,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 55 executed (118.974 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:00:59,057 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 57 +tpv.core.entities DEBUG 2024-09-14 01:00:59,097 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:00:59,097 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:00:59,102 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:00:59,117 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:00:59,135 [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 2024-09-14 01:00:59,142 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [57] queued (39.839 ms) +galaxy.jobs.handler INFO 2024-09-14 01:00:59,145 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (57) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:00:59,150 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 57 +galaxy.jobs DEBUG 2024-09-14 01:00:59,227 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [57] prepared (59.388 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:00:59,227 [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 2024-09-14 01:00:59,227 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2: samtools:1.20 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:00:59,248 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.20--h50ea8bc_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:00:59,267 [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 [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/57/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && reffa="reference.fa" && ln -s '/galaxy/server/database/objects/4/1/c/dataset_41c32e09-608f-4ddf-85e2-13bea3229eb4.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools view -b -@ $addthreads -t "$reffai" '/galaxy/server/database/objects/4/c/3/dataset_4c33dcfc-06db-4200-9078-534cadb9f3e5.dat' | samtools sort -O bam -@ $addthreads -m $addmemory"M" -o '/galaxy/server/database/objects/e/4/3/dataset_e431d350-d031-4393-a6b3-5df0c270103b.dat' -T "${TMPDIR:-.}"] +galaxy.jobs.runners DEBUG 2024-09-14 01:00:59,278 [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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:00:59,289 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:00:59,290 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2: samtools:1.20 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:00:59,307 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.20--h50ea8bc_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:01:10,662 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 57: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:01:15,203 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 57 finished +galaxy.model.metadata DEBUG 2024-09-14 01:01:15,254 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 75 +galaxy.jobs INFO 2024-09-14 01:01:15,339 [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 2024-09-14 01:01:15,383 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 57 executed (155.516 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:01:17,520 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 58 +tpv.core.entities DEBUG 2024-09-14 01:01:17,560 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:01:17,560 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:01:17,566 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:01:17,584 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:01:17,602 [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 2024-09-14 01:01:17,608 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [58] queued (42.705 ms) +galaxy.jobs.handler INFO 2024-09-14 01:01:17,612 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (58) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:01:17,617 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 58 +galaxy.jobs DEBUG 2024-09-14 01:01:17,724 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [58] prepared (86.280 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:01:17,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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' '76:/galaxy/server/database/objects/c/6/4/dataset_c640c79c-c73d-4bce-beac-b55e27344a9e_files:/galaxy/server/database/objects/c/6/4/dataset_c640c79c-c73d-4bce-beac-b55e27344a9e.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:01:17,756 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (58) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/58/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/58/galaxy_58.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-09-14 01:01:18,616 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 59 +tpv.core.entities DEBUG 2024-09-14 01:01:18,657 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:01:18,657 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:01:18,664 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:01:18,701 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:01:18,717 [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 2024-09-14 01:01:18,724 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [59] queued (60.111 ms) +galaxy.jobs.handler INFO 2024-09-14 01:01:18,729 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (59) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:01:18,733 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 59 +galaxy.jobs DEBUG 2024-09-14 01:01:18,857 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [59] prepared (104.534 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:01:18,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/59/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/59/registry.xml' '/galaxy/server/database/jobs_directory/000/59/upload_params.json' '77:/galaxy/server/database/objects/b/2/c/dataset_b2ce373b-8a50-4fdb-b724-cbaadfe6aad6_files:/galaxy/server/database/objects/b/2/c/dataset_b2ce373b-8a50-4fdb-b724-cbaadfe6aad6.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:01:18,889 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (59) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/59/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/59/galaxy_59.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:01:25,013 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 58: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:01:27,173 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 59: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:01:30,133 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 58 finished +galaxy.model.metadata DEBUG 2024-09-14 01:01:30,188 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 76 +galaxy.jobs INFO 2024-09-14 01:01:30,219 [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 2024-09-14 01:01:30,269 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 58 executed (111.390 ms) +galaxy.jobs.runners DEBUG 2024-09-14 01:01:32,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 59 finished +galaxy.model.metadata DEBUG 2024-09-14 01:01:32,274 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 77 +galaxy.jobs INFO 2024-09-14 01:01:32,317 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 59 in /galaxy/server/database/jobs_directory/000/59 +galaxy.jobs DEBUG 2024-09-14 01:01:32,360 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 59 executed (112.615 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:01:33,307 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 60 +tpv.core.entities DEBUG 2024-09-14 01:01:33,343 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:01:33,343 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:01:33,348 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:01:33,361 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:01:33,378 [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 2024-09-14 01:01:33,386 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [60] queued (38.259 ms) +galaxy.jobs.handler INFO 2024-09-14 01:01:33,389 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (60) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:01:33,394 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 60 +galaxy.jobs DEBUG 2024-09-14 01:01:33,457 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [60] prepared (48.218 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:01:33,458 [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 2024-09-14 01:01:33,458 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2: samtools:1.20 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:01:33,479 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.20--h50ea8bc_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:01:33,498 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/60/tool_script.sh] for tool command [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/60/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && reffa="reference.fa.gz" && ln -s '/galaxy/server/database/objects/b/2/c/dataset_b2ce373b-8a50-4fdb-b724-cbaadfe6aad6.dat' $reffa && { samtools faidx $reffa || { echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 && gzip -dc $reffa > reference.fa && reffa="reference.fa" && samtools faidx $reffa; } } && reffai=$reffa.fai && samtools view -b -@ $addthreads -t "$reffai" '/galaxy/server/database/objects/c/6/4/dataset_c640c79c-c73d-4bce-beac-b55e27344a9e.dat' | samtools sort -O bam -@ $addthreads -m $addmemory"M" -o '/galaxy/server/database/objects/6/6/3/dataset_66306d65-db7f-4db7-ad0a-0fe6b3d7a015.dat' -T "${TMPDIR:-.}"] +galaxy.jobs.runners DEBUG 2024-09-14 01:01:33,508 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:01:33,521 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:01:33,521 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2: samtools:1.20 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:01:33,538 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.20--h50ea8bc_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:01:38,382 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 60: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:01:43,057 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 60 finished +galaxy.model.metadata DEBUG 2024-09-14 01:01:43,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 78 +galaxy.jobs INFO 2024-09-14 01:01:43,174 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 60 in /galaxy/server/database/jobs_directory/000/60 +galaxy.jobs DEBUG 2024-09-14 01:01:43,216 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 60 executed (134.473 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:01:45,637 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 61 +tpv.core.entities DEBUG 2024-09-14 01:01:45,671 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:01:45,671 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:01:45,676 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:01:45,690 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:01:45,705 [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 2024-09-14 01:01:45,712 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [61] queued (36.136 ms) +galaxy.jobs.handler INFO 2024-09-14 01:01:45,716 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (61) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:01:45,720 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 61 +galaxy.jobs DEBUG 2024-09-14 01:01:45,805 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [61] prepared (70.711 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:01:45,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/61/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/61/registry.xml' '/galaxy/server/database/jobs_directory/000/61/upload_params.json' '79:/galaxy/server/database/objects/b/4/3/dataset_b434cb2c-2d17-4e1f-960e-91537a4ae052_files:/galaxy/server/database/objects/b/4/3/dataset_b434cb2c-2d17-4e1f-960e-91537a4ae052.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:01:45,836 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (61) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/61/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/61/galaxy_61.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-09-14 01:01:46,718 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 62 +tpv.core.entities DEBUG 2024-09-14 01:01:46,749 [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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:01:46,749 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:01:46,753 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:01:46,769 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:01:46,788 [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 2024-09-14 01:01:46,795 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [62] queued (41.270 ms) +galaxy.jobs.handler INFO 2024-09-14 01:01:46,799 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (62) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:01:46,803 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 62 +galaxy.jobs DEBUG 2024-09-14 01:01:46,905 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [62] prepared (80.862 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:01:46,923 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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' '80:/galaxy/server/database/objects/b/b/e/dataset_bbe7c712-c56e-4779-b32b-b58536491cb0_files:/galaxy/server/database/objects/b/b/e/dataset_bbe7c712-c56e-4779-b32b-b58536491cb0.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:01:46,935 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:01:54,704 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 61: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:01:55,832 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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 2024-09-14 01:01:59,674 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 61 finished +galaxy.model.metadata DEBUG 2024-09-14 01:01:59,731 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 79 +galaxy.jobs INFO 2024-09-14 01:01:59,769 [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 2024-09-14 01:01:59,816 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 61 executed (115.754 ms) +galaxy.jobs.runners DEBUG 2024-09-14 01:02:00,691 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 62 finished +galaxy.model.metadata DEBUG 2024-09-14 01:02:00,746 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 80 +galaxy.jobs INFO 2024-09-14 01:02:00,774 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 62 in /galaxy/server/database/jobs_directory/000/62 +galaxy.jobs DEBUG 2024-09-14 01:02:00,825 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 62 executed (108.930 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:02:01,090 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 63 +tpv.core.entities DEBUG 2024-09-14 01:02:01,126 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:02:01,127 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:02:01,131 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:02:01,145 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:02:01,164 [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 2024-09-14 01:02:01,173 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [63] queued (41.585 ms) +galaxy.jobs.handler INFO 2024-09-14 01:02:01,176 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (63) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:02:01,180 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 63 +galaxy.jobs DEBUG 2024-09-14 01:02:01,257 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [63] prepared (57.462 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:02:01,257 [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 2024-09-14 01:02:01,257 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2: samtools:1.20 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:02:01,282 [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:1.20--h50ea8bc_1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:02:01,303 [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 [samtools 2>&1 | grep Version > /galaxy/server/database/jobs_directory/000/63/outputs/COMMAND_VERSION 2>&1; +addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && reffa="reference.fa.gz" && ln -s '/galaxy/server/database/objects/b/b/e/dataset_bbe7c712-c56e-4779-b32b-b58536491cb0.dat' $reffa && { samtools faidx $reffa || { echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 && gzip -dc $reffa > reference.fa && reffa="reference.fa" && samtools faidx $reffa; } } && reffai=$reffa.fai && samtools view -b -@ $addthreads -t "$reffai" '/galaxy/server/database/objects/b/4/3/dataset_b434cb2c-2d17-4e1f-960e-91537a4ae052.dat' | samtools sort -O bam -@ $addthreads -m $addmemory"M" -o '/galaxy/server/database/objects/7/b/6/dataset_7b60c548-808f-4aaf-9b0e-485d44cd7737.dat' -T "${TMPDIR:-.}"] +galaxy.jobs.runners DEBUG 2024-09-14 01:02:01,318 [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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:02:01,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:02:01,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2: samtools:1.20 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:02:01,350 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/samtools:1.20--h50ea8bc_1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:02:07,011 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 63: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:02:11,731 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 63 finished +galaxy.model.metadata DEBUG 2024-09-14 01:02:11,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 81 +galaxy.jobs INFO 2024-09-14 01:02:11,864 [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 2024-09-14 01:02:11,911 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 63 executed (152.809 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:02:15,470 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 64 +tpv.core.entities DEBUG 2024-09-14 01:02:15,504 [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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:02:15,505 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:02:15,509 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:02:15,523 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:02:15,542 [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 2024-09-14 01:02:15,549 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [64] queued (39.197 ms) +galaxy.jobs.handler INFO 2024-09-14 01:02:15,552 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (64) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:02:15,557 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 64 +galaxy.jobs DEBUG 2024-09-14 01:02:15,655 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [64] prepared (80.266 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:02:15,674 [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' '82:/galaxy/server/database/objects/0/e/c/dataset_0ec80de0-a6fe-4a06-8f08-57c3644d56d6_files:/galaxy/server/database/objects/0/e/c/dataset_0ec80de0-a6fe-4a06-8f08-57c3644d56d6.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:02:15,686 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:02:23,233 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 64: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:02:27,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 64 finished +galaxy.model.metadata DEBUG 2024-09-14 01:02:27,878 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 82 +galaxy.jobs INFO 2024-09-14 01:02:27,918 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 64 in /galaxy/server/database/jobs_directory/000/64 +galaxy.jobs DEBUG 2024-09-14 01:02:27,967 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 64 executed (119.311 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:02:28,817 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 65 +tpv.core.entities DEBUG 2024-09-14 01:02:28,853 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:02:28,853 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:02:28,859 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:02:28,874 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:02:28,891 [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 2024-09-14 01:02:28,898 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [65] queued (39.292 ms) +galaxy.jobs.handler INFO 2024-09-14 01:02:28,901 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (65) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:02:28,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 65 +galaxy.jobs DEBUG 2024-09-14 01:02:28,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [65] prepared (75.026 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:02:28,999 [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 2024-09-14 01:02:28,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:02:29,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:02:29,194 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/65/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/65/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/0/e/c/dataset_0ec80de0-a6fe-4a06-8f08-57c3644d56d6.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin setGT --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz -- --target-gt '.' --new-gt '0' > '/galaxy/server/database/objects/6/4/c/dataset_64c559e1-7737-44d9-975a-b916868431a1.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:02:29,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (65) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:02:29,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:02:29,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:02:29,236 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:02:38,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 65: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:02:43,160 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 65 finished +galaxy.model.metadata DEBUG 2024-09-14 01:02:43,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 83 +galaxy.jobs INFO 2024-09-14 01:02:43,258 [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 2024-09-14 01:02:43,298 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 65 executed (113.530 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:02:45,249 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 66 +tpv.core.entities DEBUG 2024-09-14 01:02:45,283 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:02:45,283 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:02:45,288 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:02:45,301 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:02:45,319 [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 2024-09-14 01:02:45,326 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [66] queued (38.110 ms) +galaxy.jobs.handler INFO 2024-09-14 01:02:45,330 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (66) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:02:45,334 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 66 +galaxy.jobs DEBUG 2024-09-14 01:02:45,434 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [66] prepared (83.358 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:02:45,455 [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' '84:/galaxy/server/database/objects/4/a/b/dataset_4ab9d8f2-4762-4409-8dbd-7c65c8a898ca_files:/galaxy/server/database/objects/4/a/b/dataset_4ab9d8f2-4762-4409-8dbd-7c65c8a898ca.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:02:45,465 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:02:53,602 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 66: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:02:58,232 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 66 finished +galaxy.model.metadata DEBUG 2024-09-14 01:02:58,285 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 84 +galaxy.jobs INFO 2024-09-14 01:02:58,321 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 66 in /galaxy/server/database/jobs_directory/000/66 +galaxy.jobs DEBUG 2024-09-14 01:02:58,365 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 66 executed (107.785 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:02:59,715 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 67 +tpv.core.entities DEBUG 2024-09-14 01:02:59,749 [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=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:02:59,749 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:02:59,754 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:02:59,768 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:02:59,786 [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 2024-09-14 01:02:59,793 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [67] queued (38.766 ms) +galaxy.jobs.handler INFO 2024-09-14 01:02:59,796 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (67) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:02:59,801 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 67 +galaxy.jobs DEBUG 2024-09-14 01:02:59,866 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [67] prepared (49.175 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:02:59,866 [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 2024-09-14 01:02:59,867 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:02:59,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:02:59,908 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/67/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/67/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/4/a/b/dataset_4ab9d8f2-4762-4409-8dbd-7c65c8a898ca.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin setGT --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz -- --target-gt 'q' --new-gt '.' --exclude 'FMT/GQ>20' > '/galaxy/server/database/objects/8/1/c/dataset_81c09ab0-f62b-472b-adda-e824aa20d96e.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:02:59,919 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (67) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:02:59,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:02:59,932 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:02:59,949 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:03:04,754 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 67: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:03:09,466 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 67 finished +galaxy.model.metadata DEBUG 2024-09-14 01:03:09,521 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 85 +galaxy.jobs INFO 2024-09-14 01:03:09,560 [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 2024-09-14 01:03:09,606 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 67 executed (113.700 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:03:14,085 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 68 +tpv.core.entities DEBUG 2024-09-14 01:03:14,119 [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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:03:14,119 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:03:14,124 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:03:14,141 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:03:14,160 [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 2024-09-14 01:03:14,167 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [68] queued (42.500 ms) +galaxy.jobs.handler INFO 2024-09-14 01:03:14,170 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (68) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:03:14,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 68 +galaxy.jobs DEBUG 2024-09-14 01:03:14,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [68] prepared (80.712 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:03:14,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '86:/galaxy/server/database/objects/9/0/b/dataset_90bc8cb7-14e1-41de-b44e-84736db0e809_files:/galaxy/server/database/objects/9/0/b/dataset_90bc8cb7-14e1-41de-b44e-84736db0e809.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:03:14,308 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:03:23,101 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 68: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:03:28,068 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 68 finished +galaxy.model.metadata DEBUG 2024-09-14 01:03:28,126 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 86 +galaxy.jobs INFO 2024-09-14 01:03:28,166 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 68 in /galaxy/server/database/jobs_directory/000/68 +galaxy.jobs DEBUG 2024-09-14 01:03:28,220 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 68 executed (125.383 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:03:29,499 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 69 +tpv.core.entities DEBUG 2024-09-14 01:03:29,535 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:03:29,535 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:03:29,540 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:03:29,557 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:03:29,576 [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 2024-09-14 01:03:29,583 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [69] queued (43.637 ms) +galaxy.jobs.handler INFO 2024-09-14 01:03:29,587 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (69) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:03:29,591 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 69 +galaxy.jobs DEBUG 2024-09-14 01:03:29,699 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [69] prepared (90.433 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:03:29,700 [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 2024-09-14 01:03:29,700 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:03:29,722 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:03:29,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/69/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/69/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/9/0/b/dataset_90bc8cb7-14e1-41de-b44e-84736db0e809.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --variants-only --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/2/d/3/dataset_2d3b832f-33d5-42d1-8517-9fffd277ea4e.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:03:29,758 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (69) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:03:29,772 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:03:29,772 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:03:29,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:03:35,250 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 69: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:03:40,074 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 69 finished +galaxy.model.metadata DEBUG 2024-09-14 01:03:40,126 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 87 +galaxy.jobs INFO 2024-09-14 01:03:40,164 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 69 in /galaxy/server/database/jobs_directory/000/69 +galaxy.jobs DEBUG 2024-09-14 01:03:40,211 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 69 executed (111.368 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:03:42,898 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 70 +tpv.core.entities DEBUG 2024-09-14 01:03:42,933 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:03:42,934 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:03:42,939 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:03:42,954 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:03:42,971 [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 2024-09-14 01:03:42,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [70] queued (38.679 ms) +galaxy.jobs.handler INFO 2024-09-14 01:03:42,981 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (70) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:03:42,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 70 +galaxy.jobs DEBUG 2024-09-14 01:03:43,087 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [70] prepared (81.685 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:03:43,106 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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' '88:/galaxy/server/database/objects/e/b/b/dataset_ebbeee57-e587-4c2f-9418-d45c4f97df06_files:/galaxy/server/database/objects/e/b/b/dataset_ebbeee57-e587-4c2f-9418-d45c4f97df06.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:03:43,119 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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" +sqlitedict.SqliteMultithread DEBUG 2024-09-14 01:03:45,873 [pN:job_handler_0,p:8,tN:Thread-9] received: --close--, send: --no more-- +sqlitedict.SqliteMultithread DEBUG 2024-09-14 01:03:45,875 [pN:job_handler_0,p:8,tN:Thread-12] received: --close--, send: --no more-- +sqlitedict.SqliteMultithread DEBUG 2024-09-14 01:03:45,968 [pN:job_handler_0,p:8,tN:Thread-17] received: --close--, send: --no more-- +sqlitedict.SqliteMultithread DEBUG 2024-09-14 01:03:45,970 [pN:job_handler_0,p:8,tN:Thread-22] received: --close--, send: --no more-- +sqlitedict.SqliteMultithread DEBUG 2024-09-14 01:03:45,972 [pN:job_handler_0,p:8,tN:Thread-19] received: --close--, send: --no more-- +sqlitedict.SqliteMultithread DEBUG 2024-09-14 01:03:45,972 [pN:job_handler_0,p:8,tN:Thread-21] received: --close--, send: --no more-- +sqlitedict.SqliteMultithread DEBUG 2024-09-14 01:03:45,973 [pN:job_handler_0,p:8,tN:Thread-20] received: --close--, send: --no more-- +sqlitedict.SqliteMultithread DEBUG 2024-09-14 01:03:45,973 [pN:job_handler_0,p:8,tN:Thread-18] received: --close--, send: --no more-- +sqlitedict.SqliteMultithread DEBUG 2024-09-14 01:03:45,973 [pN:job_handler_0,p:8,tN:Thread-15] received: --close--, send: --no more-- +galaxy.jobs.runners.kubernetes ERROR 2024-09-14 01:03:51,175 [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/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.108.80.1:443/apis/batch/v1/namespaces/prod-24-09-14-00-32-1/jobs/gxy-pqs99 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-pqs99": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:03:51,219 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (70/gxy-pqs99) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-09-14 01:03:53,180 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 71 +tpv.core.entities DEBUG 2024-09-14 01:03:53,214 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:03:53,214 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:03:53,222 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:03:53,238 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:03:53,257 [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 2024-09-14 01:03:53,264 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [71] queued (42.063 ms) +galaxy.jobs.handler INFO 2024-09-14 01:03:53,268 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (71) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:03:53,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 71 +galaxy.jobs DEBUG 2024-09-14 01:03:53,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [71] prepared (87.605 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:03:53,398 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/71/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/71/registry.xml' '/galaxy/server/database/jobs_directory/000/71/upload_params.json' '89:/galaxy/server/database/objects/f/4/6/dataset_f46e1805-e9f8-4e9a-9ea1-cd196d038e0a_files:/galaxy/server/database/objects/f/4/6/dataset_f46e1805-e9f8-4e9a-9ea1-cd196d038e0a.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:03:53,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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.handler DEBUG 2024-09-14 01:03:54,270 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 72 +tpv.core.entities DEBUG 2024-09-14 01:03:54,304 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:03:54,304 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:03:54,309 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:03:54,321 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:03:54,341 [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 2024-09-14 01:03:54,349 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [72] queued (40.689 ms) +galaxy.jobs.handler INFO 2024-09-14 01:03:54,353 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (72) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:03:54,357 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 72 +galaxy.jobs DEBUG 2024-09-14 01:03:54,465 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [72] prepared (87.880 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:03:54,487 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '90:/galaxy/server/database/objects/4/4/1/dataset_4415ae9d-9e1b-452a-86fe-f4d0b0b052b9_files:/galaxy/server/database/objects/4/4/1/dataset_4415ae9d-9e1b-452a-86fe-f4d0b0b052b9.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:03:54,501 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (72) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/72/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/72/galaxy_72.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-09-14 01:03:55,356 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 73 +tpv.core.entities DEBUG 2024-09-14 01:03:55,384 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:03:55,384 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:03:55,388 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:03:55,402 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:03:55,418 [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 2024-09-14 01:03:55,424 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [73] queued (36.589 ms) +galaxy.jobs.handler INFO 2024-09-14 01:03:55,428 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (73) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:03:55,432 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 73 +galaxy.jobs DEBUG 2024-09-14 01:03:55,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [73] prepared (87.157 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:03:55,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/73/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/73/registry.xml' '/galaxy/server/database/jobs_directory/000/73/upload_params.json' '91:/galaxy/server/database/objects/d/2/1/dataset_d21bfe2a-02e8-4109-8e00-a59007c7bf33_files:/galaxy/server/database/objects/d/2/1/dataset_d21bfe2a-02e8-4109-8e00-a59007c7bf33.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:03:55,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (73) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/73/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/73/galaxy_73.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:04:02,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 71: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:04:03,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:04:04,311 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 73: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:04:08,933 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 71 finished +galaxy.model.metadata DEBUG 2024-09-14 01:04:09,118 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 89 +galaxy.jobs INFO 2024-09-14 01:04:09,222 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 71 in /galaxy/server/database/jobs_directory/000/71 +galaxy.jobs DEBUG 2024-09-14 01:04:09,307 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 71 executed (283.239 ms) +galaxy.jobs.runners DEBUG 2024-09-14 01:04:10,063 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 72 finished +galaxy.model.metadata DEBUG 2024-09-14 01:04:10,119 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 90 +galaxy.jobs INFO 2024-09-14 01:04:10,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 72 in /galaxy/server/database/jobs_directory/000/72 +galaxy.jobs DEBUG 2024-09-14 01:04:10,211 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 72 executed (119.996 ms) +galaxy.jobs.runners DEBUG 2024-09-14 01:04:10,833 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 73 finished +galaxy.model.metadata DEBUG 2024-09-14 01:04:10,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 91 +galaxy.jobs INFO 2024-09-14 01:04:10,919 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 73 in /galaxy/server/database/jobs_directory/000/73 +galaxy.jobs DEBUG 2024-09-14 01:04:10,974 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 73 executed (115.140 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:04:11,978 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 74 +tpv.core.entities DEBUG 2024-09-14 01:04:12,024 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:04:12,024 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:04:12,030 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:04:12,047 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:04:12,067 [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 2024-09-14 01:04:12,076 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [74] queued (46.109 ms) +galaxy.jobs.handler INFO 2024-09-14 01:04:12,080 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (74) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:04:12,084 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 74 +galaxy.jobs DEBUG 2024-09-14 01:04:12,170 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [74] prepared (66.893 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:04:12,170 [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 2024-09-14 01:04:12,171 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:04:12,192 [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-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:04:12,214 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/74/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/74/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/4/6/dataset_f46e1805-e9f8-4e9a-9ea1-cd196d038e0a.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --samples-file "/galaxy/server/database/objects/4/4/1/dataset_4415ae9d-9e1b-452a-86fe-f4d0b0b052b9.dat" --ploidy-file '/galaxy/server/database/objects/d/2/1/dataset_d21bfe2a-02e8-4109-8e00-a59007c7bf33.dat' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/2/a/6/dataset_2a6e6c11-cec3-4b08-900f-745d1d0f79f9.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:04:12,226 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (74) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:04:12,239 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:04:12,239 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:04:12,260 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:04:18,336 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 74: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:04:23,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 74 finished +galaxy.model.metadata DEBUG 2024-09-14 01:04:23,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 92 +galaxy.jobs INFO 2024-09-14 01:04:23,464 [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 2024-09-14 01:04:23,511 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 74 executed (111.167 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:04:26,382 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 75 +tpv.core.entities DEBUG 2024-09-14 01:04:26,419 [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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:04:26,420 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:04:26,426 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:04:26,445 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:04:26,466 [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 2024-09-14 01:04:26,475 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [75] queued (48.101 ms) +galaxy.jobs.handler INFO 2024-09-14 01:04:26,478 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (75) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:04:26,483 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 75 +galaxy.jobs DEBUG 2024-09-14 01:04:26,598 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [75] prepared (93.342 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:04:26,618 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/75/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/75/registry.xml' '/galaxy/server/database/jobs_directory/000/75/upload_params.json' '93:/galaxy/server/database/objects/0/1/6/dataset_0169bfe6-0746-4748-9eb6-acd70fc7c9b7_files:/galaxy/server/database/objects/0/1/6/dataset_0169bfe6-0746-4748-9eb6-acd70fc7c9b7.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:04:26,631 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (75) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/75/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/75/galaxy_75.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-09-14 01:04:27,481 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 76 +tpv.core.entities DEBUG 2024-09-14 01:04:27,514 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:04:27,515 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:04:27,520 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:04:27,537 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:04:27,558 [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 2024-09-14 01:04:27,565 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [76] queued (45.163 ms) +galaxy.jobs.handler INFO 2024-09-14 01:04:27,569 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (76) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:04:27,573 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 76 +galaxy.jobs DEBUG 2024-09-14 01:04:27,685 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [76] prepared (91.801 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:04:27,708 [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' '94:/galaxy/server/database/objects/1/7/a/dataset_17a8daa3-95a4-40f0-b5c9-34b72456c79d_files:/galaxy/server/database/objects/1/7/a/dataset_17a8daa3-95a4-40f0-b5c9-34b72456c79d.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:04:27,720 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:04:34,887 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 75: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:04:36,077 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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 2024-09-14 01:04:40,305 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 75 finished +galaxy.model.metadata DEBUG 2024-09-14 01:04:40,371 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 93 +galaxy.jobs INFO 2024-09-14 01:04:40,411 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 75 in /galaxy/server/database/jobs_directory/000/75 +galaxy.jobs DEBUG 2024-09-14 01:04:40,462 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 75 executed (127.562 ms) +galaxy.jobs.runners DEBUG 2024-09-14 01:04:41,079 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 76 finished +galaxy.model.metadata DEBUG 2024-09-14 01:04:41,126 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 94 +galaxy.jobs INFO 2024-09-14 01:04:41,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 76 in /galaxy/server/database/jobs_directory/000/76 +galaxy.jobs DEBUG 2024-09-14 01:04:41,207 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 76 executed (106.022 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:04:41,884 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 77 +tpv.core.entities DEBUG 2024-09-14 01:04:41,923 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:04:41,924 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:04:41,929 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:04:41,945 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:04:41,963 [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 2024-09-14 01:04:41,972 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [77] queued (43.434 ms) +galaxy.jobs.handler INFO 2024-09-14 01:04:41,976 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (77) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:04:41,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 77 +galaxy.jobs DEBUG 2024-09-14 01:04:42,059 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [77] prepared (61.412 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:04:42,059 [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 2024-09-14 01:04:42,059 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:04:42,241 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:04:42,260 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/77/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/77/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/0/1/6/dataset_0169bfe6-0746-4748-9eb6-acd70fc7c9b7.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -c --pval-threshold 0.5 --ploidy-file '/galaxy/server/database/objects/1/7/a/dataset_17a8daa3-95a4-40f0-b5c9-34b72456c79d.dat' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/3/3/5/dataset_3354dc69-b987-4dde-a2c6-85b31ef2c0fc.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:04:42,271 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (77) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/77/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/77/galaxy_77.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:04:42,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:04:42,282 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:04:42,300 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:04:46,186 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 77: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:04:50,967 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 77 finished +galaxy.model.metadata DEBUG 2024-09-14 01:04:51,018 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 95 +galaxy.jobs INFO 2024-09-14 01:04:51,052 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 77 in /galaxy/server/database/jobs_directory/000/77 +galaxy.jobs DEBUG 2024-09-14 01:04:51,097 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 77 executed (105.741 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:04:54,353 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 79, 78 +tpv.core.entities DEBUG 2024-09-14 01:04:54,383 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:04:54,383 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:04:54,387 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:04:54,400 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:04:54,416 [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 2024-09-14 01:04:54,423 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [78] queued (35.043 ms) +galaxy.jobs.handler INFO 2024-09-14 01:04:54,426 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (78) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:04:54,431 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 78 +tpv.core.entities DEBUG 2024-09-14 01:04:54,440 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:04:54,441 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:04:54,445 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:04:54,462 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:04:54,493 [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 2024-09-14 01:04:54,500 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [79] queued (54.615 ms) +galaxy.jobs.handler INFO 2024-09-14 01:04:54,506 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (79) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:04:54,509 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 79 +galaxy.jobs DEBUG 2024-09-14 01:04:54,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [78] prepared (93.862 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:04:54,565 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/78/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/78/registry.xml' '/galaxy/server/database/jobs_directory/000/78/upload_params.json' '96:/galaxy/server/database/objects/2/8/0/dataset_280c6e28-ddda-4b08-b70b-63b33c482628_files:/galaxy/server/database/objects/2/8/0/dataset_280c6e28-ddda-4b08-b70b-63b33c482628.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:04:54,577 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (78) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/78/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/78/galaxy_78.ec; sh -c "exit $return_code" +galaxy.jobs DEBUG 2024-09-14 01:04:54,620 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [79] prepared (90.283 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:04:54,642 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/79/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/79/registry.xml' '/galaxy/server/database/jobs_directory/000/79/upload_params.json' '97:/galaxy/server/database/objects/e/8/c/dataset_e8ce517b-35d8-4f05-a500-27ed2a854b76_files:/galaxy/server/database/objects/e/8/c/dataset_e8ce517b-35d8-4f05-a500-27ed2a854b76.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:04:54,654 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (79) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/79/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/79/galaxy_79.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:05:02,915 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 78: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:05:02,947 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 79: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:05:07,764 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 78 finished +galaxy.jobs.runners DEBUG 2024-09-14 01:05:07,816 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 79 finished +galaxy.model.metadata DEBUG 2024-09-14 01:05:07,832 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 96 +galaxy.jobs INFO 2024-09-14 01:05:07,876 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 78 in /galaxy/server/database/jobs_directory/000/78 +galaxy.model.metadata DEBUG 2024-09-14 01:05:07,877 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 97 +galaxy.jobs INFO 2024-09-14 01:05:07,919 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 79 in /galaxy/server/database/jobs_directory/000/79 +galaxy.jobs DEBUG 2024-09-14 01:05:07,942 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 78 executed (143.828 ms) +galaxy.jobs DEBUG 2024-09-14 01:05:07,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 79 executed (134.549 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:05:08,798 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 80 +tpv.core.entities DEBUG 2024-09-14 01:05:08,838 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:05:08,838 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:05:08,843 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:05:08,854 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:05:08,869 [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 2024-09-14 01:05:08,875 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [80] queued (32.271 ms) +galaxy.jobs.handler INFO 2024-09-14 01:05:08,878 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (80) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:05:08,883 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 80 +galaxy.jobs DEBUG 2024-09-14 01:05:08,949 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [80] prepared (49.833 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:05:08,950 [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 2024-09-14 01:05:08,950 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:05:08,969 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:05:08,989 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/80/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/80/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/2/8/0/dataset_280c6e28-ddda-4b08-b70b-63b33c482628.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -c --pval-threshold 0.5 --ploidy-file '/galaxy/server/database/objects/e/8/c/dataset_e8ce517b-35d8-4f05-a500-27ed2a854b76.dat' --annotate INFO/PV4 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/a/5/1/dataset_a51cf330-c1c4-4b13-8f9d-c8e5ff207911.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:05:09,000 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (80) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/80/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/80/galaxy_80.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:05:09,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:05:09,012 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:05:09,030 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:05:14,061 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 80: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:05:18,717 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 80 finished +galaxy.model.metadata DEBUG 2024-09-14 01:05:18,774 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 98 +galaxy.jobs INFO 2024-09-14 01:05:18,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 80 in /galaxy/server/database/jobs_directory/000/80 +galaxy.jobs DEBUG 2024-09-14 01:05:18,902 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 80 executed (160.664 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:05:22,153 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 81 +tpv.core.entities DEBUG 2024-09-14 01:05:22,183 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:05:22,184 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:05:22,188 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:05:22,200 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:05:22,218 [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 2024-09-14 01:05:22,224 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [81] queued (35.648 ms) +galaxy.jobs.handler INFO 2024-09-14 01:05:22,227 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (81) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:05:22,231 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 81 +galaxy.jobs DEBUG 2024-09-14 01:05:22,324 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [81] prepared (75.501 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:05:22,342 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '99:/galaxy/server/database/objects/c/c/b/dataset_ccb9add7-6130-4226-b9ff-91874809a4d9_files:/galaxy/server/database/objects/c/c/b/dataset_ccb9add7-6130-4226-b9ff-91874809a4d9.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:05:22,354 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:05:30,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 81: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:05:35,260 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 81 finished +galaxy.model.metadata DEBUG 2024-09-14 01:05:35,321 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 99 +galaxy.jobs INFO 2024-09-14 01:05:35,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 81 in /galaxy/server/database/jobs_directory/000/81 +galaxy.jobs DEBUG 2024-09-14 01:05:35,409 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 81 executed (123.278 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:05:36,516 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 82 +tpv.core.entities DEBUG 2024-09-14 01:05:36,546 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:05:36,547 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:05:36,552 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:05:36,566 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:05:36,584 [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 2024-09-14 01:05:36,592 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [82] queued (39.286 ms) +galaxy.jobs.handler INFO 2024-09-14 01:05:36,596 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (82) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:05:36,600 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 82 +galaxy.jobs DEBUG 2024-09-14 01:05:36,663 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [82] prepared (46.408 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:05:36,664 [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 2024-09-14 01:05:36,664 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:05:36,683 [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/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:05:36,702 [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 [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/82/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/c/c/b/dataset_ccb9add7-6130-4226-b9ff-91874809a4d9.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --regions-overlap 1 --variants-only --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/9/f/4/dataset_9f43a52e-df3f-4799-bda3-48f718656361.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:05:36,713 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (82) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:05:36,725 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:05:36,725 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:05:36,740 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:05:41,647 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 82: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:05:46,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 82 finished +galaxy.model.metadata DEBUG 2024-09-14 01:05:46,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 100 +galaxy.jobs INFO 2024-09-14 01:05:46,319 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 82 in /galaxy/server/database/jobs_directory/000/82 +galaxy.jobs DEBUG 2024-09-14 01:05:46,371 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 82 executed (121.607 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:05:49,862 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 83 +tpv.core.entities DEBUG 2024-09-14 01:05:49,892 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:05:49,892 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:05:49,896 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:05:49,913 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:05:49,929 [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 2024-09-14 01:05:49,935 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [83] queued (38.867 ms) +galaxy.jobs.handler INFO 2024-09-14 01:05:49,939 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (83) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:05:49,943 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 83 +galaxy.jobs DEBUG 2024-09-14 01:05:50,048 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [83] prepared (84.439 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:05:50,069 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/83/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/83/registry.xml' '/galaxy/server/database/jobs_directory/000/83/upload_params.json' '101:/galaxy/server/database/objects/5/c/7/dataset_5c73108f-7db9-4e2e-9762-31df7ea70502_files:/galaxy/server/database/objects/5/c/7/dataset_5c73108f-7db9-4e2e-9762-31df7ea70502.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:05:50,082 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (83) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/83/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/83/galaxy_83.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:05:57,916 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 83: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:06:02,761 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 83 finished +galaxy.model.metadata DEBUG 2024-09-14 01:06:02,809 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 101 +galaxy.jobs INFO 2024-09-14 01:06:02,844 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 83 in /galaxy/server/database/jobs_directory/000/83 +galaxy.jobs DEBUG 2024-09-14 01:06:02,889 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 83 executed (105.039 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:06:04,218 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 84 +tpv.core.entities DEBUG 2024-09-14 01:06:04,251 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:06:04,251 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:06:04,257 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:06:04,274 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:06:04,293 [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 2024-09-14 01:06:04,300 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [84] queued (41.991 ms) +galaxy.jobs.handler INFO 2024-09-14 01:06:04,303 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (84) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:06:04,308 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 84 +galaxy.jobs DEBUG 2024-09-14 01:06:04,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [84] prepared (49.675 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:06:04,375 [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 2024-09-14 01:06:04,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:06:04,394 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:06:04,413 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/84/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/84/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/5/c/7/dataset_5c73108f-7db9-4e2e-9762-31df7ea70502.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --group-samples - --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/f/7/4/dataset_f7421e87-a418-4b27-9fa0-562c91b117c2.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:06:04,422 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (84) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/84/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/84/galaxy_84.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:06:04,434 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:06:04,435 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:06:04,452 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:06:09,043 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 84: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:06:13,720 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 84 finished +galaxy.model.metadata DEBUG 2024-09-14 01:06:13,781 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 102 +galaxy.jobs INFO 2024-09-14 01:06:13,819 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 84 in /galaxy/server/database/jobs_directory/000/84 +galaxy.jobs DEBUG 2024-09-14 01:06:13,864 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 84 executed (116.225 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:06:16,543 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 85 +tpv.core.entities DEBUG 2024-09-14 01:06:16,574 [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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:06:16,574 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:06:16,579 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:06:16,592 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:06:16,609 [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 2024-09-14 01:06:16,616 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [85] queued (36.869 ms) +galaxy.jobs.handler INFO 2024-09-14 01:06:16,620 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (85) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:06:16,624 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 85 +galaxy.jobs DEBUG 2024-09-14 01:06:16,716 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [85] prepared (75.932 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:06:16,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/85/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/85/registry.xml' '/galaxy/server/database/jobs_directory/000/85/upload_params.json' '103:/galaxy/server/database/objects/b/8/5/dataset_b851b4ac-86be-4622-bbe1-cc1c4d60f388_files:/galaxy/server/database/objects/b/8/5/dataset_b851b4ac-86be-4622-bbe1-cc1c4d60f388.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:06:16,746 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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.handler DEBUG 2024-09-14 01:06:17,622 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 86 +tpv.core.entities DEBUG 2024-09-14 01:06:17,654 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:06:17,654 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:06:17,659 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:06:17,674 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:06:17,689 [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 2024-09-14 01:06:17,695 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [86] queued (36.070 ms) +galaxy.jobs.handler INFO 2024-09-14 01:06:17,698 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (86) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:06:17,702 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 86 +galaxy.jobs DEBUG 2024-09-14 01:06:17,795 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [86] prepared (76.249 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:06:17,814 [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' '104:/galaxy/server/database/objects/f/9/a/dataset_f9ab92a9-992d-4798-8921-d967a0352f8b_files:/galaxy/server/database/objects/f/9/a/dataset_f9ab92a9-992d-4798-8921-d967a0352f8b.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:06:17,826 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:06:24,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 85: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:06:25,574 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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 2024-09-14 01:06:29,554 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 85 finished +galaxy.model.metadata DEBUG 2024-09-14 01:06:29,610 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 103 +galaxy.jobs INFO 2024-09-14 01:06:29,644 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 85 in /galaxy/server/database/jobs_directory/000/85 +galaxy.jobs DEBUG 2024-09-14 01:06:29,688 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 85 executed (107.407 ms) +galaxy.jobs.runners DEBUG 2024-09-14 01:06:30,504 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 86 finished +galaxy.model.metadata DEBUG 2024-09-14 01:06:30,560 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 104 +galaxy.jobs INFO 2024-09-14 01:06:30,593 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 86 in /galaxy/server/database/jobs_directory/000/86 +galaxy.jobs DEBUG 2024-09-14 01:06:30,645 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 86 executed (116.029 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:06:32,048 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 87 +tpv.core.entities DEBUG 2024-09-14 01:06:32,084 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:06:32,085 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:06:32,089 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:06:32,103 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:06:32,119 [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 2024-09-14 01:06:32,126 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [87] queued (37.202 ms) +galaxy.jobs.handler INFO 2024-09-14 01:06:32,130 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (87) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:06:32,134 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 87 +galaxy.jobs DEBUG 2024-09-14 01:06:32,211 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [87] prepared (59.143 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:06:32,211 [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 2024-09-14 01:06:32,212 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:06:32,234 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:06:32,254 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/87/tool_script.sh] for tool command [bcftools 2>&1 | grep 'Version:' > /galaxy/server/database/jobs_directory/000/87/outputs/COMMAND_VERSION 2>&1; +export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/b/8/5/dataset_b851b4ac-86be-4622-bbe1-cc1c4d60f388.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --targets-file "/galaxy/server/database/objects/f/9/a/dataset_f9ab92a9-992d-4798-8921-d967a0352f8b.dat" --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/a/1/a/dataset_a1aa4eef-f0a9-4302-bc82-9e4cd2d6448a.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:06:32,268 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (87) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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.tool_util.deps.containers INFO 2024-09-14 01:06:32,280 [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 2024-09-14 01:06:32,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5: mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a +galaxy.tool_util.deps.containers INFO 2024-09-14 01:06:32,299 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-b99184dc2d32592dd62a87fa4a796c61585788e6:07602ea99d759e160674ea07c369efffcc80577a-0,type=docker]] +galaxy.jobs.runners.kubernetes ERROR 2024-09-14 01:06:36,745 [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/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.108.80.1:443/apis/batch/v1/namespaces/prod-24-09-14-00-32-1/jobs/gxy-tbxfz + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-tbxfz": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:06:36,788 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (87/gxy-tbxfz) Terminated at user's request +galaxy.jobs.handler DEBUG 2024-09-14 01:06:40,274 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 88 +tpv.core.entities DEBUG 2024-09-14 01:06:40,304 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:06:40,304 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:06:40,308 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:06:40,321 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:06:40,337 [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 2024-09-14 01:06:40,343 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [88] queued (35.616 ms) +galaxy.jobs.handler INFO 2024-09-14 01:06:40,346 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (88) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:06:40,350 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 88 +galaxy.jobs DEBUG 2024-09-14 01:06:40,449 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [88] prepared (80.165 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:06:40,469 [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' '106:/galaxy/server/database/objects/6/f/0/dataset_6f06394e-3de7-4b30-bd5d-a8022de72d66_files:/galaxy/server/database/objects/6/f/0/dataset_6f06394e-3de7-4b30-bd5d-a8022de72d66.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:06:40,481 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:06:48,120 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 88: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:06:52,783 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 88 finished +galaxy.model.metadata DEBUG 2024-09-14 01:06:52,839 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 106 +galaxy.jobs INFO 2024-09-14 01:06:52,874 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 88 in /galaxy/server/database/jobs_directory/000/88 +galaxy.jobs DEBUG 2024-09-14 01:06:52,921 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 88 executed (111.790 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:06:53,618 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 89 +tpv.core.entities DEBUG 2024-09-14 01:06:53,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:06:53,655 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:06:53,659 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:06:53,675 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:06:53,692 [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 2024-09-14 01:06:53,699 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [89] queued (40.198 ms) +galaxy.jobs.handler INFO 2024-09-14 01:06:53,704 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (89) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:06:53,709 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 89 +galaxy.jobs DEBUG 2024-09-14 01:06:53,791 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [89] prepared (62.521 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:06:53,791 [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 2024-09-14 01:06:53,792 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:06:53,967 [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/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:06:53,988 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/89/tool_script.sh] for tool command [vcfbreakmulti '/galaxy/server/database/objects/6/f/0/dataset_6f06394e-3de7-4b30-bd5d-a8022de72d66.dat' > '/galaxy/server/database/objects/5/1/6/dataset_516cbe10-a6d6-4358-b2fe-a26efc52862f.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:06:54,002 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:06:54,014 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:06:54,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:06:54,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:07:02,320 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 89: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:07:07,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 89 finished +galaxy.model.metadata DEBUG 2024-09-14 01:07:07,094 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 107 +galaxy.jobs INFO 2024-09-14 01:07:07,129 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 89 in /galaxy/server/database/jobs_directory/000/89 +galaxy.jobs DEBUG 2024-09-14 01:07:07,175 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 89 executed (109.806 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:07:10,045 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 90 +tpv.core.entities DEBUG 2024-09-14 01:07:10,083 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:07:10,083 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:07:10,088 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:07:10,105 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:07:10,122 [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 2024-09-14 01:07:10,128 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [90] queued (39.363 ms) +galaxy.jobs.handler INFO 2024-09-14 01:07:10,132 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (90) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:07:10,136 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 90 +galaxy.jobs DEBUG 2024-09-14 01:07:10,247 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [90] prepared (90.309 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:07:10,271 [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' '108:/galaxy/server/database/objects/2/c/9/dataset_2c9c5a73-d4bb-4aee-8f81-d39b5c7e6501_files:/galaxy/server/database/objects/2/c/9/dataset_2c9c5a73-d4bb-4aee-8f81-d39b5c7e6501.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:07:10,286 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:07:18,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 90: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:07:23,253 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 90 finished +galaxy.model.metadata DEBUG 2024-09-14 01:07:23,309 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 108 +galaxy.jobs INFO 2024-09-14 01:07:23,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 90 in /galaxy/server/database/jobs_directory/000/90 +galaxy.jobs DEBUG 2024-09-14 01:07:23,396 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 90 executed (114.631 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:07:24,414 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 91 +tpv.core.entities DEBUG 2024-09-14 01:07:24,447 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:07:24,448 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:07:24,453 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:07:24,467 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:07:24,484 [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 2024-09-14 01:07:24,491 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [91] queued (37.954 ms) +galaxy.jobs.handler INFO 2024-09-14 01:07:24,494 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (91) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:07:24,498 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 91 +galaxy.jobs DEBUG 2024-09-14 01:07:24,567 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [91] prepared (53.776 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:07:24,568 [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 2024-09-14 01:07:24,568 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:07:24,593 [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/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:07:24,615 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/91/tool_script.sh] for tool command [vcfcreatemulti '/galaxy/server/database/objects/2/c/9/dataset_2c9c5a73-d4bb-4aee-8f81-d39b5c7e6501.dat' > '/galaxy/server/database/objects/5/b/5/dataset_5b5457c8-be0e-4075-ad84-a140b4d63aaa.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:07:24,628 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (91) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/91/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/91/galaxy_91.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:07:24,642 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:07:24,642 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:07:24,660 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:07:29,804 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 91: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:07:34,437 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 91 finished +galaxy.model.metadata DEBUG 2024-09-14 01:07:34,500 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 109 +galaxy.jobs INFO 2024-09-14 01:07:34,538 [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 2024-09-14 01:07:34,582 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 91 executed (114.401 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:07:38,780 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 92 +tpv.core.entities DEBUG 2024-09-14 01:07:38,822 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:07:38,823 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:07:38,828 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:07:38,845 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:07:38,862 [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 2024-09-14 01:07:38,870 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [92] queued (41.511 ms) +galaxy.jobs.handler INFO 2024-09-14 01:07:38,874 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (92) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:07:38,878 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 92 +galaxy.jobs DEBUG 2024-09-14 01:07:38,985 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [92] prepared (88.981 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:07:39,006 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '110:/galaxy/server/database/objects/8/4/e/dataset_84e39377-0100-40a9-ba12-9ca6dd14878f_files:/galaxy/server/database/objects/8/4/e/dataset_84e39377-0100-40a9-ba12-9ca6dd14878f.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:07:39,016 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (92) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/92/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/92/galaxy_92.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:07:47,099 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 92: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:07:51,787 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 92 finished +galaxy.model.metadata DEBUG 2024-09-14 01:07:51,839 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 110 +galaxy.jobs INFO 2024-09-14 01:07:51,875 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 92 in /galaxy/server/database/jobs_directory/000/92 +galaxy.jobs DEBUG 2024-09-14 01:07:51,925 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 92 executed (114.462 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:07:53,215 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 93 +tpv.core.entities DEBUG 2024-09-14 01:07:53,251 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:07:53,252 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:07:53,255 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:07:53,268 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:07:53,286 [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 2024-09-14 01:07:53,294 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [93] queued (38.436 ms) +galaxy.jobs.handler INFO 2024-09-14 01:07:53,298 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (93) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:07:53,302 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 93 +galaxy.jobs DEBUG 2024-09-14 01:07:53,375 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [93] prepared (55.499 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:07:53,376 [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 2024-09-14 01:07:53,376 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:07:53,396 [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 2024-09-14 01:07:53,415 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/93/tool_script.sh] for tool command [vcfkeepsamples '/galaxy/server/database/objects/8/4/e/dataset_84e39377-0100-40a9-ba12-9ca6dd14878f.dat' "NA00001" "NA00003" > '/galaxy/server/database/objects/4/2/d/dataset_42df1ec7-6bca-4aed-8966-66ea16ac07bf.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:07:53,425 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (93) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/93/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/93/galaxy_93.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:07:53,436 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:07:53,436 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0: vcflib:1.0.0_rc3 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:07:53,455 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/vcflib:1.0.0_rc3--py37hc088bd4_0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:07:58,273 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 93: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:08:02,955 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 93 finished +galaxy.model.metadata DEBUG 2024-09-14 01:08:03,014 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 111 +galaxy.jobs INFO 2024-09-14 01:08:03,046 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 93 in /galaxy/server/database/jobs_directory/000/93 +galaxy.jobs DEBUG 2024-09-14 01:08:03,086 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 93 executed (101.846 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:08:07,584 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 94 +tpv.core.entities DEBUG 2024-09-14 01:08:07,614 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:08:07,615 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:08:07,619 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:08:07,635 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:08:07,653 [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 2024-09-14 01:08:07,661 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [94] queued (40.940 ms) +galaxy.jobs.handler INFO 2024-09-14 01:08:07,665 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (94) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:08:07,670 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 94 +galaxy.jobs DEBUG 2024-09-14 01:08:07,783 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [94] prepared (93.978 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:08:07,807 [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' '112:/galaxy/server/database/objects/6/2/b/dataset_62b11c17-ec6c-4bc4-8a13-8e3dc741307e_files:/galaxy/server/database/objects/6/2/b/dataset_62b11c17-ec6c-4bc4-8a13-8e3dc741307e.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:08:07,820 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:08:15,454 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 94: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:08:20,348 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 94 finished +galaxy.model.metadata DEBUG 2024-09-14 01:08:20,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 112 +galaxy.jobs INFO 2024-09-14 01:08:20,438 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 94 in /galaxy/server/database/jobs_directory/000/94 +galaxy.jobs DEBUG 2024-09-14 01:08:20,491 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 94 executed (114.939 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:08:20,953 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 95 +tpv.core.entities DEBUG 2024-09-14 01:08:20,995 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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_occupancy/poretools_occupancy/.*, abstract=False, cores=1, mem=11.4, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:08:20,995 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:08:21,000 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:08:21,018 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:08:21,038 [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 2024-09-14 01:08:21,047 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [95] queued (45.995 ms) +galaxy.jobs.handler INFO 2024-09-14 01:08:21,051 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (95) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:08:21,055 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 95 +galaxy.jobs DEBUG 2024-09-14 01:08:21,139 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [95] prepared (64.415 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:08:21,139 [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 2024-09-14 01:08:21,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:08:21,310 [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/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:08:21,332 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/95/tool_script.sh] for tool command [export MPLBACKEND="agg" && poretools occupancy '/galaxy/server/database/objects/6/2/b/dataset_62b11c17-ec6c-4bc4-8a13-8e3dc741307e.dat' --saveas occupancy.png --plot-type read_count && mv occupancy.png '/galaxy/server/database/objects/4/b/3/dataset_4b3c64f9-a60d-461a-9d32-070e41cada4e.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:08:21,346 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:08:21,359 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:08:21,360 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:08:21,378 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:08:51,258 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 95: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:08:56,304 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 95 finished +galaxy.model.metadata DEBUG 2024-09-14 01:08:56,369 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 113 +galaxy.util WARNING 2024-09-14 01:08:56,372 [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/b/3/dataset_4b3c64f9-a60d-461a-9d32-070e41cada4e.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/b/3/dataset_4b3c64f9-a60d-461a-9d32-070e41cada4e.dat' +galaxy.jobs INFO 2024-09-14 01:08:56,403 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 95 in /galaxy/server/database/jobs_directory/000/95 +galaxy.jobs DEBUG 2024-09-14 01:08:56,456 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 95 executed (120.401 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:08:59,971 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 96 +tpv.core.entities DEBUG 2024-09-14 01:09:00,004 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:09:00,005 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:09:00,009 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:09:00,024 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:09:00,042 [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 2024-09-14 01:09:00,051 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [96] queued (42.492 ms) +galaxy.jobs.handler INFO 2024-09-14 01:09:00,055 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (96) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:09:00,058 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 96 +galaxy.jobs DEBUG 2024-09-14 01:09:00,171 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [96] prepared (94.500 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:09:00,192 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] 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' '114:/galaxy/server/database/objects/a/3/d/dataset_a3d686e3-815f-4a4b-8be3-f9a3dce3945e_files:/galaxy/server/database/objects/a/3/d/dataset_a3d686e3-815f-4a4b-8be3-f9a3dce3945e.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:09:00,204 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (96) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/96/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/96/galaxy_96.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:09:07,367 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 96: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:09:12,449 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 96 finished +galaxy.model.metadata DEBUG 2024-09-14 01:09:12,517 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 114 +galaxy.jobs INFO 2024-09-14 01:09:12,555 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 96 in /galaxy/server/database/jobs_directory/000/96 +galaxy.jobs DEBUG 2024-09-14 01:09:12,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 96 executed (126.364 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:09:13,337 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 97 +tpv.core.entities DEBUG 2024-09-14 01:09:13,369 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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_occupancy/poretools_occupancy/.*, abstract=False, cores=1, mem=11.4, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:09:13,370 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:09:13,374 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:09:13,390 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:09:13,406 [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 2024-09-14 01:09:13,414 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [97] queued (39.488 ms) +galaxy.jobs.handler INFO 2024-09-14 01:09:13,419 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (97) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:09:13,422 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 97 +galaxy.jobs DEBUG 2024-09-14 01:09:13,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [97] prepared (55.063 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:09:13,497 [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 2024-09-14 01:09:13,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:09:13,522 [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 2024-09-14 01:09:13,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/97/tool_script.sh] for tool command [export MPLBACKEND="agg" && poretools occupancy '/galaxy/server/database/objects/a/3/d/dataset_a3d686e3-815f-4a4b-8be3-f9a3dce3945e.dat' --saveas occupancy.pdf --plot-type total_bp && mv occupancy.pdf '/galaxy/server/database/objects/1/c/a/dataset_1ca7c8ab-b06c-4fce-9238-a1f3e4e61b28.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:09:13,558 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:09:13,571 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:09:13,571 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1: poretools:0.6.1a1 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:09:13,590 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/poretools:0.6.1a1--py_8,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:09:20,564 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 97: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:09:25,575 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 97 finished +galaxy.model.metadata DEBUG 2024-09-14 01:09:25,633 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 115 +galaxy.util WARNING 2024-09-14 01:09:25,638 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/1/c/a/dataset_1ca7c8ab-b06c-4fce-9238-a1f3e4e61b28.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/1/c/a/dataset_1ca7c8ab-b06c-4fce-9238-a1f3e4e61b28.dat' +galaxy.jobs INFO 2024-09-14 01:09:25,674 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 97 in /galaxy/server/database/jobs_directory/000/97 +galaxy.jobs DEBUG 2024-09-14 01:09:25,729 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 97 executed (127.542 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:09:29,800 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 98 +tpv.core.entities DEBUG 2024-09-14 01:09:29,842 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:09:29,843 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:09:29,848 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:09:29,869 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:09:29,890 [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 2024-09-14 01:09:29,897 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [98] queued (49.310 ms) +galaxy.jobs.handler INFO 2024-09-14 01:09:29,900 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (98) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:09:29,906 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 98 +galaxy.jobs DEBUG 2024-09-14 01:09:30,024 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [98] prepared (97.323 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:09:30,049 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/98/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/98/registry.xml' '/galaxy/server/database/jobs_directory/000/98/upload_params.json' '116:/galaxy/server/database/objects/d/4/3/dataset_d438d13f-b491-496e-8b2d-f2b243b8546d_files:/galaxy/server/database/objects/d/4/3/dataset_d438d13f-b491-496e-8b2d-f2b243b8546d.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:09:30,067 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (98) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/98/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/98/galaxy_98.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:09:37,726 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 98: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:09:42,473 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 98 finished +galaxy.model.metadata DEBUG 2024-09-14 01:09:42,535 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 116 +galaxy.jobs INFO 2024-09-14 01:09:42,572 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 98 in /galaxy/server/database/jobs_directory/000/98 +galaxy.jobs DEBUG 2024-09-14 01:09:42,618 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 98 executed (116.516 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:09:43,195 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 99 +tpv.core.entities DEBUG 2024-09-14 01:09:43,234 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/.*, abstract=False, cores=1, mem=25, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:09:43,234 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:09:43,240 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:09:43,259 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:09:43,278 [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 2024-09-14 01:09:43,287 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [99] queued (46.613 ms) +galaxy.jobs.handler INFO 2024-09-14 01:09:43,291 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (99) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:09:43,296 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 99 +galaxy.jobs DEBUG 2024-09-14 01:09:43,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [99] prepared (71.377 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:09:43,387 [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 2024-09-14 01:09:43,387 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:09:43,583 [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-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:09:43,605 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/99/tool_script.sh] for tool command [plotHeatmap --version > /galaxy/server/database/jobs_directory/000/99/outputs/COMMAND_VERSION 2>&1; +plotHeatmap --matrixFile '/galaxy/server/database/objects/d/4/3/dataset_d438d13f-b491-496e-8b2d-f2b243b8546d.dat' --outFileName '/galaxy/server/database/objects/a/d/c/dataset_adc68014-a820-4b22-be2e-162dac3e0139.dat' --plotFileFormat 'png'] +galaxy.jobs.runners DEBUG 2024-09-14 01:09:43,618 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (99) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/99/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/99/galaxy_99.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:09:43,633 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:09:43,633 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:09:43,653 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:10:06,256 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 99: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 DEBUG 2024-09-14 01:10:10,919 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 99 finished +galaxy.model.metadata DEBUG 2024-09-14 01:10:10,972 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 117 +galaxy.util WARNING 2024-09-14 01:10:10,977 [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/a/d/c/dataset_adc68014-a820-4b22-be2e-162dac3e0139.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/a/d/c/dataset_adc68014-a820-4b22-be2e-162dac3e0139.dat' +galaxy.jobs INFO 2024-09-14 01:10:11,001 [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.objectstore CRITICAL 2024-09-14 01:10:11,049 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'matplotlib' +galaxy.jobs DEBUG 2024-09-14 01:10:11,049 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 99 executed (105.695 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:10:13,942 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 100 +tpv.core.entities DEBUG 2024-09-14 01:10:13,976 [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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:10:13,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:10:13,982 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:10:13,997 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:10:14,017 [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 2024-09-14 01:10:14,024 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [100] queued (42.425 ms) +galaxy.jobs.handler INFO 2024-09-14 01:10:14,028 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (100) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:10:14,032 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 100 +galaxy.jobs DEBUG 2024-09-14 01:10:14,140 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [100] prepared (89.416 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:10:14,159 [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' '118:/galaxy/server/database/objects/7/0/5/dataset_705df5d3-8c62-4995-8742-ae99529407ce_files:/galaxy/server/database/objects/7/0/5/dataset_705df5d3-8c62-4995-8742-ae99529407ce.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:10:14,171 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:10:22,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 100: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:10:27,280 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 100 finished +galaxy.model.metadata DEBUG 2024-09-14 01:10:27,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 118 +galaxy.jobs INFO 2024-09-14 01:10:27,377 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 100 in /galaxy/server/database/jobs_directory/000/100 +galaxy.jobs DEBUG 2024-09-14 01:10:27,422 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 100 executed (110.687 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:10:28,318 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 101 +tpv.core.entities DEBUG 2024-09-14 01:10:28,355 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/.*, abstract=False, cores=1, mem=25, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:10:28,356 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:10:28,361 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:10:28,374 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:10:28,391 [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 2024-09-14 01:10:28,398 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [101] queued (37.286 ms) +galaxy.jobs.handler INFO 2024-09-14 01:10:28,401 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (101) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:10:28,405 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 101 +galaxy.jobs DEBUG 2024-09-14 01:10:28,471 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [101] prepared (52.511 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:10:28,472 [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 2024-09-14 01:10:28,472 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:10:28,497 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:10:28,518 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/101/tool_script.sh] for tool command [plotHeatmap --version > /galaxy/server/database/jobs_directory/000/101/outputs/COMMAND_VERSION 2>&1; +plotHeatmap --matrixFile '/galaxy/server/database/objects/7/0/5/dataset_705df5d3-8c62-4995-8742-ae99529407ce.dat' --outFileName '/galaxy/server/database/objects/4/d/1/dataset_4d1f5276-3b0a-4117-9d7d-f68eb141f3dd.dat' --plotFileFormat 'png' --sortRegions 'descend' --sortUsing 'mean' --averageTypeSummaryPlot 'mean' --plotType 'lines' --missingDataColor 'black' --alpha '1.0' --xAxisLabel 'distance from TSS (bp)' --yAxisLabel 'genes' --heatmapWidth 7.5 --heatmapHeight 25.0 --whatToShow 'heatmap and colorbar' --startLabel 'TSS' --endLabel 'TES' --refPointLabel 'TSS' --legendLocation 'best' --labelRotation '0'] +galaxy.jobs.runners DEBUG 2024-09-14 01:10:28,531 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (101) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/101/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/101/galaxy_101.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:10:28,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:10:28,543 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:10:28,561 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:10:34,987 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 101: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:10:39,739 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 101 finished +galaxy.model.metadata DEBUG 2024-09-14 01:10:39,786 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 119 +galaxy.util WARNING 2024-09-14 01:10:39,792 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/4/d/1/dataset_4d1f5276-3b0a-4117-9d7d-f68eb141f3dd.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/d/1/dataset_4d1f5276-3b0a-4117-9d7d-f68eb141f3dd.dat' +galaxy.jobs INFO 2024-09-14 01:10:39,817 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 101 in /galaxy/server/database/jobs_directory/000/101 +galaxy.objectstore CRITICAL 2024-09-14 01:10:39,858 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'matplotlib' +galaxy.jobs DEBUG 2024-09-14 01:10:39,859 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 101 executed (95.526 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:10:43,717 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 102 +tpv.core.entities DEBUG 2024-09-14 01:10:43,750 [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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:10:43,751 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:10:43,755 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:10:43,768 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:10:43,785 [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 2024-09-14 01:10:43,792 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [102] queued (36.498 ms) +galaxy.jobs.handler INFO 2024-09-14 01:10:43,795 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (102) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:10:43,800 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 102 +galaxy.jobs DEBUG 2024-09-14 01:10:43,898 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [102] prepared (81.843 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:10:43,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/102/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/102/registry.xml' '/galaxy/server/database/jobs_directory/000/102/upload_params.json' '120:/galaxy/server/database/objects/1/f/2/dataset_1f23dafd-d951-4a12-b9e3-4a38224f484e_files:/galaxy/server/database/objects/1/f/2/dataset_1f23dafd-d951-4a12-b9e3-4a38224f484e.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:10:43,930 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (102) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/102/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/102/galaxy_102.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:10:52,337 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 102: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:10:56,865 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 102 finished +galaxy.model.metadata DEBUG 2024-09-14 01:10:56,919 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 120 +galaxy.jobs INFO 2024-09-14 01:10:56,955 [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 2024-09-14 01:10:57,006 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 102 executed (115.945 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:10:58,083 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 103 +tpv.core.entities DEBUG 2024-09-14 01:10:58,120 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/.*, abstract=False, cores=1, mem=20, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:10:58,121 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:10:58,125 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:10:58,141 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:10:58,162 [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 2024-09-14 01:10:58,170 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [103] queued (44.844 ms) +galaxy.jobs.handler INFO 2024-09-14 01:10:58,173 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (103) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:10:58,178 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 103 +galaxy.jobs DEBUG 2024-09-14 01:10:58,269 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [103] prepared (71.735 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:10:58,270 [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 2024-09-14 01:10:58,270 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:10:58,292 [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:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:10:58,315 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/103/tool_script.sh] for tool command [plotProfile --version > /galaxy/server/database/jobs_directory/000/103/outputs/COMMAND_VERSION 2>&1; +plotProfile --matrixFile "/galaxy/server/database/objects/1/f/2/dataset_1f23dafd-d951-4a12-b9e3-4a38224f484e.dat" --outFileName "/galaxy/server/database/objects/4/0/8/dataset_4084c388-b579-4d96-8f18-2068c455f459.dat" --plotFileFormat 'png'] +galaxy.jobs.runners DEBUG 2024-09-14 01:10:58,328 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (103) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/103/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/103/galaxy_103.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:10:58,341 [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 2024-09-14 01:10:58,341 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:10:58,358 [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:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1,type=docker]] +galaxy.jobs.runners.kubernetes ERROR 2024-09-14 01:11:04,605 [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/python3.10/site-packages/pykube/http.py", line 437, in raise_for_status + resp.raise_for_status() + File "/galaxy/server/.venv/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status + raise HTTPError(http_error_msg, response=self) +requests.exceptions.HTTPError: 409 Client Error: Conflict for url: https://10.108.80.1:443/apis/batch/v1/namespaces/prod-24-09-14-00-32-1/jobs/gxy-mgxft + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 817, in _handle_job_failure + self.__cleanup_k8s_job(job) + File "/galaxy/server/lib/galaxy/jobs/runners/kubernetes.py", line 824, in __cleanup_k8s_job + delete_job(job, k8s_cleanup_job) + File "/galaxy/server/lib/galaxy/jobs/runners/util/pykube_util.py", line 107, in delete_job + job.scale(replicas=0) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/mixins.py", line 30, in scale + self.update() + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 165, in update + self.patch(self.obj, subresource=subresource) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/objects.py", line 157, in patch + self.api.raise_for_status(r) + File "/galaxy/server/.venv/lib/python3.10/site-packages/pykube/http.py", line 444, in raise_for_status + raise HTTPError(resp.status_code, payload["message"]) +pykube.exceptions.HTTPError: Operation cannot be fulfilled on jobs.batch "gxy-mgxft": the object has been modified; please apply your changes to the latest version and try again +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:11:04,657 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (103/gxy-mgxft) Terminated at user's request +galaxy.util WARNING 2024-09-14 01:11:04,715 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/4/0/8/dataset_4084c388-b579-4d96-8f18-2068c455f459.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/4/0/8/dataset_4084c388-b579-4d96-8f18-2068c455f459.dat' +galaxy.objectstore CRITICAL 2024-09-14 01:11:04,742 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] None delete error [Errno 13] Permission denied: 'matplotlib' +galaxy.jobs.handler DEBUG 2024-09-14 01:11:07,344 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 104 +tpv.core.entities DEBUG 2024-09-14 01:11:07,375 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:11:07,376 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:11:07,380 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:11:07,394 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:11:07,409 [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 2024-09-14 01:11:07,414 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [104] queued (33.773 ms) +galaxy.jobs.handler INFO 2024-09-14 01:11:07,417 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (104) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:11:07,422 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 104 +galaxy.jobs DEBUG 2024-09-14 01:11:07,531 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [104] prepared (85.965 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:11:07,552 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] 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' '122:/galaxy/server/database/objects/1/8/f/dataset_18fd5a19-c90a-4551-9f2d-29c13ca03e07_files:/galaxy/server/database/objects/1/8/f/dataset_18fd5a19-c90a-4551-9f2d-29c13ca03e07.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:11:07,565 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (104) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/104/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/104/galaxy_104.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:11:14,904 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 104: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:11:19,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 104 finished +galaxy.model.metadata DEBUG 2024-09-14 01:11:19,717 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 122 +galaxy.jobs INFO 2024-09-14 01:11:19,745 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 104 in /galaxy/server/database/jobs_directory/000/104 +galaxy.jobs DEBUG 2024-09-14 01:11:19,789 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 104 executed (97.072 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:11:20,669 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 105 +tpv.core.entities DEBUG 2024-09-14 01:11:20,701 [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=toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/.*, abstract=False, cores=1, mem=20, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:11:20,702 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:11:20,705 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:11:20,716 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:11:20,733 [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 2024-09-14 01:11:20,739 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [105] queued (33.744 ms) +galaxy.jobs.handler INFO 2024-09-14 01:11:20,742 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (105) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:11:20,746 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 105 +galaxy.jobs DEBUG 2024-09-14 01:11:20,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [105] prepared (46.969 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:11:20,807 [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 2024-09-14 01:11:20,807 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:11:20,826 [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:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:11:20,846 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/105/tool_script.sh] for tool command [plotProfile --version > /galaxy/server/database/jobs_directory/000/105/outputs/COMMAND_VERSION 2>&1; +plotProfile --matrixFile "/galaxy/server/database/objects/1/8/f/dataset_18fd5a19-c90a-4551-9f2d-29c13ca03e07.dat" --outFileName "/galaxy/server/database/objects/e/3/8/dataset_e385b1a2-eb88-4eb4-a2d1-11b673338e16.dat" --plotFileFormat 'png' --startLabel 'TSS' --endLabel 'TES' --averageType 'mean' --plotHeight 5 --plotWidth 11 --plotType lines --legendLocation 'best' --labelRotation '0' --outFileNameData '/galaxy/server/database/objects/7/f/8/dataset_7f8a3c03-a2e9-47f8-b9ad-ee351625b489.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:11:20,862 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (105) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/105/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/105/galaxy_105.ec; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:11:20,875 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:11:20,875 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0: mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:11:20,891 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:bcea566aaf2a8cd09765df369b45c50e0b7e9f18-1,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:11:27,066 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 105: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:11:31,897 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 105 finished +galaxy.model.metadata DEBUG 2024-09-14 01:11:31,950 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 123 +galaxy.model.metadata DEBUG 2024-09-14 01:11:31,959 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 124 +galaxy.util WARNING 2024-09-14 01:11:31,967 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/e/3/8/dataset_e385b1a2-eb88-4eb4-a2d1-11b673338e16.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/e/3/8/dataset_e385b1a2-eb88-4eb4-a2d1-11b673338e16.dat' +galaxy.util WARNING 2024-09-14 01:11:31,967 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/7/f/8/dataset_7f8a3c03-a2e9-47f8-b9ad-ee351625b489.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/7/f/8/dataset_7f8a3c03-a2e9-47f8-b9ad-ee351625b489.dat' +galaxy.jobs INFO 2024-09-14 01:11:32,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 105 in /galaxy/server/database/jobs_directory/000/105 +galaxy.objectstore CRITICAL 2024-09-14 01:11:32,058 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] None delete error [Errno 13] Permission denied: 'matplotlib' +galaxy.jobs DEBUG 2024-09-14 01:11:32,058 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 105 executed (136.264 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:11:37,091 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 106 +tpv.core.entities DEBUG 2024-09-14 01:11:37,123 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:11:37,124 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:11:37,128 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:11:37,142 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:11:37,159 [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 2024-09-14 01:11:37,167 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [106] queued (38.807 ms) +galaxy.jobs.handler INFO 2024-09-14 01:11:37,172 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (106) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:11:37,176 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 106 +galaxy.jobs DEBUG 2024-09-14 01:11:37,268 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [106] prepared (74.145 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:11:37,287 [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' '125:/galaxy/server/database/objects/3/7/2/dataset_372a16ea-307d-46fa-b66f-484437879aef_files:/galaxy/server/database/objects/3/7/2/dataset_372a16ea-307d-46fa-b66f-484437879aef.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:11:37,301 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:11:45,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 106: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:11:50,089 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 106 finished +galaxy.model.metadata DEBUG 2024-09-14 01:11:50,145 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 125 +galaxy.jobs INFO 2024-09-14 01:11:50,177 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 106 in /galaxy/server/database/jobs_directory/000/106 +galaxy.jobs DEBUG 2024-09-14 01:11:50,226 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 106 executed (111.953 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:11:51,459 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 107 +tpv.core.entities DEBUG 2024-09-14 01:11:51,492 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/.*, abstract=False, cores=1, mem=15.2, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:11:51,493 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:11:51,497 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:11:51,509 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:11:51,526 [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 2024-09-14 01:11:51,532 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [107] queued (34.566 ms) +galaxy.jobs.handler INFO 2024-09-14 01:11:51,536 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (107) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:11:51,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 107 +galaxy.jobs DEBUG 2024-09-14 01:11:51,620 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [107] prepared (60.062 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:11:51,620 [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 2024-09-14 01:11:51,620 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:11:51,852 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:11:51,871 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/107/tool_script.sh] for tool command [lofreq version | grep version | cut -d ' ' -f 2 > /galaxy/server/database/jobs_directory/000/107/outputs/COMMAND_VERSION 2>&1; +lofreq filter -i /galaxy/server/database/objects/3/7/2/dataset_372a16ea-307d-46fa-b66f-484437879aef.dat --no-defaults --verbose -Q 38 -K 20 -v 10 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001 -o filtered.vcf] +galaxy.jobs.runners DEBUG 2024-09-14 01:11:51,885 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (107) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/107/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/107/galaxy_107.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/107/working/filtered.vcf" ] ; then cp "/galaxy/server/database/jobs_directory/000/107/working/filtered.vcf" "/galaxy/server/database/objects/3/1/7/dataset_317a0b8a-c855-460b-9d1a-21ac1603bcb3.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:11:51,897 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:11:51,897 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:11:51,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:12:01,614 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 107: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:12:06,297 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 107 finished +galaxy.model.metadata DEBUG 2024-09-14 01:12:06,358 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 126 +galaxy.util WARNING 2024-09-14 01:12:06,364 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/3/1/7/dataset_317a0b8a-c855-460b-9d1a-21ac1603bcb3.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/3/1/7/dataset_317a0b8a-c855-460b-9d1a-21ac1603bcb3.dat' +galaxy.jobs INFO 2024-09-14 01:12:06,390 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 107 in /galaxy/server/database/jobs_directory/000/107 +galaxy.jobs DEBUG 2024-09-14 01:12:06,437 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 107 executed (113.810 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:12:08,890 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 108 +tpv.core.entities DEBUG 2024-09-14 01:12:08,920 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:12:08,921 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:12:08,924 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:12:08,938 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:12:08,955 [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 2024-09-14 01:12:08,962 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [108] queued (37.811 ms) +galaxy.jobs.handler INFO 2024-09-14 01:12:08,965 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (108) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:12:08,970 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 108 +galaxy.jobs DEBUG 2024-09-14 01:12:09,072 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [108] prepared (84.335 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:12:09,093 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/108/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/108/registry.xml' '/galaxy/server/database/jobs_directory/000/108/upload_params.json' '127:/galaxy/server/database/objects/b/b/7/dataset_bb79af39-540f-476a-8499-ce98d1bb4930_files:/galaxy/server/database/objects/b/b/7/dataset_bb79af39-540f-476a-8499-ce98d1bb4930.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:12:09,105 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (108) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/108/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/108/galaxy_108.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:12:17,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 108: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:12:22,601 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 108 finished +galaxy.model.metadata DEBUG 2024-09-14 01:12:22,657 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 127 +galaxy.jobs INFO 2024-09-14 01:12:22,690 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 108 in /galaxy/server/database/jobs_directory/000/108 +galaxy.jobs DEBUG 2024-09-14 01:12:22,739 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 108 executed (114.417 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:12:23,244 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 109 +tpv.core.entities DEBUG 2024-09-14 01:12:23,281 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/.*, abstract=False, cores=1, mem=15.2, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:12:23,282 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:12:23,286 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:12:23,301 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:12:23,318 [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 2024-09-14 01:12:23,327 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [109] queued (40.287 ms) +galaxy.jobs.handler INFO 2024-09-14 01:12:23,330 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (109) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:12:23,335 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 109 +galaxy.jobs DEBUG 2024-09-14 01:12:23,404 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [109] prepared (50.042 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:12:23,404 [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 2024-09-14 01:12:23,404 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:12:23,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:12:23,451 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/109/tool_script.sh] for tool command [lofreq version | grep version | cut -d ' ' -f 2 > /galaxy/server/database/jobs_directory/000/109/outputs/COMMAND_VERSION 2>&1; +lofreq filter -i /galaxy/server/database/objects/b/b/7/dataset_bb79af39-540f-476a-8499-ce98d1bb4930.dat --no-defaults --verbose --only-snvs -q bonf -r 0.01 -s 66 -v 10 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001 -o filtered.vcf] +galaxy.jobs.runners DEBUG 2024-09-14 01:12:23,469 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (109) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/109/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/109/galaxy_109.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/109/working/filtered.vcf" ] ; then cp "/galaxy/server/database/jobs_directory/000/109/working/filtered.vcf" "/galaxy/server/database/objects/f/c/5/dataset_fc537fb9-1af0-4abb-ac6b-c6d2c675d2f8.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:12:23,483 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:12:23,484 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:12:23,503 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:12:27,976 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 109: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:12:32,766 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 109 finished +galaxy.model.metadata DEBUG 2024-09-14 01:12:32,826 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 128 +galaxy.util WARNING 2024-09-14 01:12:32,837 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/f/c/5/dataset_fc537fb9-1af0-4abb-ac6b-c6d2c675d2f8.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/f/c/5/dataset_fc537fb9-1af0-4abb-ac6b-c6d2c675d2f8.dat' +galaxy.jobs INFO 2024-09-14 01:12:32,869 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 109 in /galaxy/server/database/jobs_directory/000/109 +galaxy.jobs DEBUG 2024-09-14 01:12:32,925 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 109 executed (133.707 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:12:35,584 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 110 +tpv.core.entities DEBUG 2024-09-14 01:12:35,619 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:12:35,619 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:12:35,623 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:12:35,638 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:12:35,655 [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 2024-09-14 01:12:35,662 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [110] queued (38.035 ms) +galaxy.jobs.handler INFO 2024-09-14 01:12:35,665 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (110) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:12:35,669 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 110 +galaxy.jobs DEBUG 2024-09-14 01:12:35,774 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [110] prepared (86.791 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:12:35,794 [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 [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/110/registry.xml' '/galaxy/server/database/jobs_directory/000/110/upload_params.json' '129:/galaxy/server/database/objects/2/b/9/dataset_2b9714b6-244b-4f44-99c5-d96ed5ed26bb_files:/galaxy/server/database/objects/2/b/9/dataset_2b9714b6-244b-4f44-99c5-d96ed5ed26bb.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:12:35,806 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:12:43,116 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 110: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:12:47,678 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 110 finished +galaxy.model.metadata DEBUG 2024-09-14 01:12:47,735 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 129 +galaxy.jobs INFO 2024-09-14 01:12:47,772 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 110 in /galaxy/server/database/jobs_directory/000/110 +galaxy.jobs DEBUG 2024-09-14 01:12:47,820 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 110 executed (116.675 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:12:48,936 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 111 +tpv.core.entities DEBUG 2024-09-14 01:12:48,975 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/.*, abstract=False, cores=1, mem=15.2, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:12:48,976 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:12:48,981 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:12:48,997 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:12:49,016 [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 2024-09-14 01:12:49,025 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [111] queued (44.557 ms) +galaxy.jobs.handler INFO 2024-09-14 01:12:49,030 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (111) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:12:49,033 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 111 +galaxy.jobs DEBUG 2024-09-14 01:12:49,098 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [111] prepared (45.247 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:12:49,098 [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 2024-09-14 01:12:49,098 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:12:49,119 [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/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:12:49,138 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/111/tool_script.sh] for tool command [lofreq version | grep version | cut -d ' ' -f 2 > /galaxy/server/database/jobs_directory/000/111/outputs/COMMAND_VERSION 2>&1; +lofreq filter -i /galaxy/server/database/objects/2/b/9/dataset_2b9714b6-244b-4f44-99c5-d96ed5ed26bb.dat --no-defaults --verbose --print-all -Q 38 -K 20 -v 10 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001 -o filtered.vcf] +galaxy.jobs.runners DEBUG 2024-09-14 01:12:49,151 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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; +if [ -f "/galaxy/server/database/jobs_directory/000/111/working/filtered.vcf" ] ; then cp "/galaxy/server/database/jobs_directory/000/111/working/filtered.vcf" "/galaxy/server/database/objects/f/a/9/dataset_fa906c50-95ff-404f-8ac9-e2034872902d.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:12:49,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:12:49,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0: lofreq:2.1.5 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:12:49,183 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/lofreq:2.1.5--py312he57d009_12,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:12:54,276 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 111: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:12:59,010 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 111 finished +galaxy.model.metadata DEBUG 2024-09-14 01:12:59,062 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 130 +galaxy.util WARNING 2024-09-14 01:12:59,069 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/f/a/9/dataset_fa906c50-95ff-404f-8ac9-e2034872902d.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/f/a/9/dataset_fa906c50-95ff-404f-8ac9-e2034872902d.dat' +galaxy.jobs INFO 2024-09-14 01:12:59,094 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 111 in /galaxy/server/database/jobs_directory/000/111 +galaxy.jobs DEBUG 2024-09-14 01:12:59,144 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 111 executed (108.623 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:13:02,452 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 112 +tpv.core.entities DEBUG 2024-09-14 01:13:02,484 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:13:02,485 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:13:02,489 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:13:02,503 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:13:02,519 [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 2024-09-14 01:13:02,525 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [112] queued (36.493 ms) +galaxy.jobs.handler INFO 2024-09-14 01:13:02,529 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (112) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:13:02,533 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 112 +galaxy.jobs DEBUG 2024-09-14 01:13:02,629 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [112] prepared (80.768 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:13:02,648 [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' '131:/galaxy/server/database/objects/3/d/a/dataset_3da24e97-7ec8-4b05-8355-23ca0794c723_files:/galaxy/server/database/objects/3/d/a/dataset_3da24e97-7ec8-4b05-8355-23ca0794c723.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:13:02,660 [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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:13:10,499 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 112: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:13:15,215 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 112 finished +galaxy.model.metadata DEBUG 2024-09-14 01:13:15,272 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 131 +galaxy.jobs INFO 2024-09-14 01:13:15,305 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 112 in /galaxy/server/database/jobs_directory/000/112 +galaxy.jobs DEBUG 2024-09-14 01:13:15,350 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 112 executed (108.426 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:13:15,802 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 113 +tpv.core.entities DEBUG 2024-09-14 01:13:15,843 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/salmon/salmon/.*, abstract=False, cores=6, mem=70, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:13:15,844 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:13:15,849 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:13:15,863 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:13:15,883 [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 2024-09-14 01:13:15,892 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [113] queued (43.473 ms) +galaxy.jobs.handler INFO 2024-09-14 01:13:15,897 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (113) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:13:15,900 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 113 +galaxy.jobs DEBUG 2024-09-14 01:13:16,009 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [113] prepared (94.655 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:13:16,010 [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 2024-09-14 01:13:16,010 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1: mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:13:16,205 [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-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:13:16,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/113/tool_script.sh] for tool command [mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/3/d/a/dataset_3da24e97-7ec8-4b05-8355-23ca0794c723.dat' && ln -s /galaxy/server/database/objects/3/d/a/dataset_3da24e97-7ec8-4b05-8355-23ca0794c723.dat ./single.fasta && salmon quant --index './index' --libType U --unmatedReads ./single.fasta --threads "${GALAXY_SLOTS:-4}" --writeMappings=./output/samout.sam --incompatPrior '0.0' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '100' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '1e-05' -o ./output && samtools sort -@ ${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam ./output/samout.sam] +galaxy.jobs.runners DEBUG 2024-09-14 01:13:16,244 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (113) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; +if [ -f "/galaxy/server/database/jobs_directory/000/113/working/output/quant.sf" ] ; then cp "/galaxy/server/database/jobs_directory/000/113/working/output/quant.sf" "/galaxy/server/database/objects/4/4/3/dataset_44357ab7-cf8e-49dc-9ead-fe2492d3662c.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/113/working/output/bamout.bam" ] ; then cp "/galaxy/server/database/jobs_directory/000/113/working/output/bamout.bam" "/galaxy/server/database/objects/a/2/b/dataset_a2b4fd54-4e08-4407-bf50-d29c5625abc9.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:13:16,257 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:13:16,257 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1: mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:13:16,278 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:13:38,098 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 113: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:13:42,991 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 113 finished +galaxy.model.metadata DEBUG 2024-09-14 01:13:43,059 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 132 +galaxy.model.metadata DEBUG 2024-09-14 01:13:43,073 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 133 +galaxy.util WARNING 2024-09-14 01:13:43,124 [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/4/4/3/dataset_44357ab7-cf8e-49dc-9ead-fe2492d3662c.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/4/4/3/dataset_44357ab7-cf8e-49dc-9ead-fe2492d3662c.dat' +galaxy.util WARNING 2024-09-14 01:13:43,124 [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/a/2/b/dataset_a2b4fd54-4e08-4407-bf50-d29c5625abc9.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/a/2/b/dataset_a2b4fd54-4e08-4407-bf50-d29c5625abc9.dat' +galaxy.jobs INFO 2024-09-14 01:13:43,156 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 113 in /galaxy/server/database/jobs_directory/000/113 +galaxy.objectstore CRITICAL 2024-09-14 01:13:43,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'cmd_info.json' +galaxy.jobs DEBUG 2024-09-14 01:13:43,195 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 113 executed (173.082 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:13:45,541 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 114 +tpv.core.entities DEBUG 2024-09-14 01:13:45,575 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:13:45,576 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:13:45,581 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:13:45,597 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:13:45,615 [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 2024-09-14 01:13:45,622 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [114] queued (41.098 ms) +galaxy.jobs.handler INFO 2024-09-14 01:13:45,626 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (114) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:13:45,631 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 114 +galaxy.jobs DEBUG 2024-09-14 01:13:45,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [114] prepared (94.845 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:13:45,770 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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' '134:/galaxy/server/database/objects/6/3/f/dataset_63f66a26-8968-4a36-8a38-81c06d448f0a_files:/galaxy/server/database/objects/6/3/f/dataset_63f66a26-8968-4a36-8a38-81c06d448f0a.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:13:45,783 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (114) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/114/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/114/galaxy_114.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:13:54,269 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 114: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:13:59,128 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 114 finished +galaxy.model.metadata DEBUG 2024-09-14 01:13:59,190 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 134 +galaxy.jobs INFO 2024-09-14 01:13:59,229 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 114 in /galaxy/server/database/jobs_directory/000/114 +galaxy.jobs DEBUG 2024-09-14 01:13:59,283 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 114 executed (124.150 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:13:59,932 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 115 +tpv.core.entities DEBUG 2024-09-14 01:13:59,976 [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=toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/.*, abstract=False, cores=6, mem=70, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:13:59,977 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:13:59,982 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:13:59,999 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:14:00,020 [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 2024-09-14 01:14:00,027 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [115] queued (44.802 ms) +galaxy.jobs.handler INFO 2024-09-14 01:14:00,031 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (115) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:14:00,035 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 115 +galaxy.jobs DEBUG 2024-09-14 01:14:00,123 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [115] prepared (66.057 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:14:00,124 [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 2024-09-14 01:14:00,124 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1: mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:14:00,147 [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-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:14:00,170 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/115/tool_script.sh] for tool command [mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/6/3/f/dataset_63f66a26-8968-4a36-8a38-81c06d448f0a.dat' && ln -s /galaxy/server/database/objects/6/3/f/dataset_63f66a26-8968-4a36-8a38-81c06d448f0a.dat ./single.fasta && salmon quant --index './index' --libType U --unmatedReads ./single.fasta --threads "${GALAXY_SLOTS:-4}" --incompatPrior '0.0' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '100' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '1e-05' -o ./output] +galaxy.jobs.runners DEBUG 2024-09-14 01:14:00,186 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (115) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/115/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/115/galaxy_115.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/115/working/output/quant.sf" ] ; then cp "/galaxy/server/database/jobs_directory/000/115/working/output/quant.sf" "/galaxy/server/database/objects/5/f/0/dataset_5f0e78b7-19ef-4886-a58c-1c22e07fdb79.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:14:00,199 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:14:00,199 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1: mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:14:00,221 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:14:07,427 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 115: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:14:12,208 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 115 finished +galaxy.model.metadata DEBUG 2024-09-14 01:14:12,265 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 135 +galaxy.util WARNING 2024-09-14 01:14:12,275 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/5/f/0/dataset_5f0e78b7-19ef-4886-a58c-1c22e07fdb79.dat, group remains grp.struct_group(gr_name='root', gr_passwd='x', gr_gid=0, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/5/f/0/dataset_5f0e78b7-19ef-4886-a58c-1c22e07fdb79.dat' +galaxy.jobs INFO 2024-09-14 01:14:12,310 [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.objectstore CRITICAL 2024-09-14 01:14:12,343 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'cmd_info.json' +galaxy.jobs DEBUG 2024-09-14 01:14:12,344 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 115 executed (105.438 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:14:14,337 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 116 +tpv.core.entities DEBUG 2024-09-14 01:14:14,370 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:14:14,371 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:14:14,376 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:14:14,390 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:14:14,406 [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 2024-09-14 01:14:14,412 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [116] queued (35.430 ms) +galaxy.jobs.handler INFO 2024-09-14 01:14:14,415 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (116) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:14:14,418 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 116 +galaxy.jobs DEBUG 2024-09-14 01:14:14,516 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [116] prepared (81.077 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:14:14,534 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/116/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/116/registry.xml' '/galaxy/server/database/jobs_directory/000/116/upload_params.json' '136:/galaxy/server/database/objects/0/8/d/dataset_08d44003-a573-41ec-b62e-688862d1ed8f_files:/galaxy/server/database/objects/0/8/d/dataset_08d44003-a573-41ec-b62e-688862d1ed8f.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:14:14,546 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:14:22,621 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 116: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:14:27,265 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 116 finished +galaxy.model.metadata DEBUG 2024-09-14 01:14:27,324 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 136 +galaxy.jobs INFO 2024-09-14 01:14:27,364 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 116 in /galaxy/server/database/jobs_directory/000/116 +galaxy.jobs DEBUG 2024-09-14 01:14:27,417 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 116 executed (125.218 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:14:28,722 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 117 +tpv.core.entities DEBUG 2024-09-14 01:14:28,760 [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/bgruening/salmon/salmon/.*, abstract=False, cores=6, mem=70, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:14:28,761 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:14:28,767 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:14:28,783 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:14:28,823 [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 2024-09-14 01:14:28,833 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [117] queued (66.063 ms) +galaxy.jobs.handler INFO 2024-09-14 01:14:28,837 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (117) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:14:28,842 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 117 +galaxy.jobs DEBUG 2024-09-14 01:14:28,916 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [117] prepared (53.914 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:14:28,916 [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 2024-09-14 01:14:28,917 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1: mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:14:28,941 [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-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:14:28,965 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/117/tool_script.sh] for tool command [mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/0/8/d/dataset_08d44003-a573-41ec-b62e-688862d1ed8f.dat' && ln -s /galaxy/server/database/objects/0/8/d/dataset_08d44003-a573-41ec-b62e-688862d1ed8f.dat ./single.fasta && salmon quant --index './index' --libType U --unmatedReads ./single.fasta --threads "${GALAXY_SLOTS:-4}" --incompatPrior '0.0' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '100' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '1e-05' -o ./output] +galaxy.jobs.runners DEBUG 2024-09-14 01:14:28,980 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (117) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; +if [ -f "/galaxy/server/database/jobs_directory/000/117/working/output/quant.sf" ] ; then cp "/galaxy/server/database/jobs_directory/000/117/working/output/quant.sf" "/galaxy/server/database/objects/a/0/f/dataset_a0f7eb43-1680-46d0-bfec-ba26c3659da1.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:14:28,992 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:14:28,992 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1: mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:14:29,013 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:14:34,913 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 117: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:14:39,602 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 117 finished +galaxy.model.metadata DEBUG 2024-09-14 01:14:39,666 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 137 +galaxy.util WARNING 2024-09-14 01:14:39,674 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/a/0/f/dataset_a0f7eb43-1680-46d0-bfec-ba26c3659da1.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/0/f/dataset_a0f7eb43-1680-46d0-bfec-ba26c3659da1.dat' +galaxy.jobs INFO 2024-09-14 01:14:39,707 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 117 in /galaxy/server/database/jobs_directory/000/117 +galaxy.objectstore CRITICAL 2024-09-14 01:14:39,743 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'cmd_info.json' +galaxy.jobs DEBUG 2024-09-14 01:14:39,744 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 117 executed (110.504 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:14:43,139 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 118 +tpv.core.entities DEBUG 2024-09-14 01:14:43,172 [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:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:14:43,173 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:14:43,178 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:14:43,193 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:14:43,210 [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 2024-09-14 01:14:43,217 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [118] queued (39.610 ms) +galaxy.jobs.handler INFO 2024-09-14 01:14:43,223 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (118) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:14:43,225 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 118 +galaxy.jobs DEBUG 2024-09-14 01:14:43,331 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [118] prepared (86.648 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:14:43,352 [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' '138:/galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89_files:/galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:14:43,365 [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.handler DEBUG 2024-09-14 01:14:44,225 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 119 +tpv.core.entities DEBUG 2024-09-14 01:14:44,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:14:44,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:14:44,266 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:14:44,281 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:14:44,295 [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 2024-09-14 01:14:44,302 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [119] queued (35.937 ms) +galaxy.jobs.handler INFO 2024-09-14 01:14:44,305 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (119) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:14:44,309 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 119 +galaxy.jobs DEBUG 2024-09-14 01:14:44,406 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [119] prepared (80.970 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:14:44,426 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Built script [/galaxy/server/database/jobs_directory/000/119/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/119/registry.xml' '/galaxy/server/database/jobs_directory/000/119/upload_params.json' '139:/galaxy/server/database/objects/3/f/9/dataset_3f98742b-13bf-4a63-b43c-e12943fc60b3_files:/galaxy/server/database/objects/3/f/9/dataset_3f98742b-13bf-4a63-b43c-e12943fc60b3.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:14:44,438 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (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 $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:14:52,338 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 118: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:14:53,440 [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 2024-09-14 01:14:57,284 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 118 finished +galaxy.model.metadata DEBUG 2024-09-14 01:14:57,337 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 138 +galaxy.jobs INFO 2024-09-14 01:14:57,398 [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 2024-09-14 01:14:57,447 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 118 executed (137.831 ms) +galaxy.jobs.runners DEBUG 2024-09-14 01:14:58,196 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 119 finished +galaxy.model.metadata DEBUG 2024-09-14 01:14:58,249 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 139 +galaxy.jobs INFO 2024-09-14 01:14:58,282 [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 2024-09-14 01:14:58,332 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 119 executed (110.212 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:14:59,627 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 120 +tpv.core.entities DEBUG 2024-09-14 01:14:59,665 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/salmon/salmon/.*, abstract=False, cores=6, mem=70, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:14:59,666 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:14:59,670 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:14:59,684 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:14:59,703 [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 2024-09-14 01:14:59,710 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [120] queued (39.749 ms) +galaxy.jobs.handler INFO 2024-09-14 01:14:59,714 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (120) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:14:59,719 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 120 +galaxy.jobs DEBUG 2024-09-14 01:14:59,801 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [120] prepared (63.283 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:14:59,802 [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 2024-09-14 01:14:59,802 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1: mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:14:59,980 [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-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:15:00,004 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/120/tool_script.sh] for tool command [salmon quant -t '/galaxy/server/database/objects/3/f/9/dataset_3f98742b-13bf-4a63-b43c-e12943fc60b3.dat' -l 'U' -a '/galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat' --threads "${GALAXY_SLOTS:-4}" --noErrorModel --numErrorBins '5' --sampleOut --sampleUnaligned --incompatPrior '0.0' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '100' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '1e-05' -o ./output && samtools sort -@ ${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam ./output/postSample.bam] +galaxy.jobs.runners DEBUG 2024-09-14 01:15:00,031 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (120) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/120/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/120/galaxy_120.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/120/working/output/quant.sf" ] ; then cp "/galaxy/server/database/jobs_directory/000/120/working/output/quant.sf" "/galaxy/server/database/objects/9/7/2/dataset_972ea182-a315-4243-a8ed-f418494b7f6b.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/120/working/output/bamout.bam" ] ; then cp "/galaxy/server/database/jobs_directory/000/120/working/output/bamout.bam" "/galaxy/server/database/objects/3/6/5/dataset_3650dd27-e490-4cb2-8a06-c0979282d02b.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:15:00,044 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:15:00,045 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1: mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:15:00,068 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:15:06,723 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 120: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:15:11,512 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 120 finished +galaxy.model.metadata DEBUG 2024-09-14 01:15:11,577 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 140 +galaxy.model.metadata DEBUG 2024-09-14 01:15:11,589 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 141 +galaxy.util WARNING 2024-09-14 01:15:11,643 [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/9/7/2/dataset_972ea182-a315-4243-a8ed-f418494b7f6b.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/9/7/2/dataset_972ea182-a315-4243-a8ed-f418494b7f6b.dat' +galaxy.util WARNING 2024-09-14 01:15:11,644 [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/3/6/5/dataset_3650dd27-e490-4cb2-8a06-c0979282d02b.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/3/6/5/dataset_3650dd27-e490-4cb2-8a06-c0979282d02b.dat' +galaxy.jobs INFO 2024-09-14 01:15:11,672 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 120 in /galaxy/server/database/jobs_directory/000/120 +galaxy.objectstore CRITICAL 2024-09-14 01:15:11,714 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'cmd_info.json' +galaxy.jobs DEBUG 2024-09-14 01:15:11,714 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 120 executed (172.148 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:15:15,029 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 121 +tpv.core.entities DEBUG 2024-09-14 01:15:15,064 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:15:15,065 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:15:15,071 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:15:15,086 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:15:15,105 [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 2024-09-14 01:15:15,113 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [121] queued (41.949 ms) +galaxy.jobs.handler INFO 2024-09-14 01:15:15,117 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (121) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:15:15,122 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Starting queue_job for job 121 +galaxy.jobs DEBUG 2024-09-14 01:15:15,233 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Job wrapper for Job [121] prepared (93.546 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:15:15,255 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Built script [/galaxy/server/database/jobs_directory/000/121/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/121/registry.xml' '/galaxy/server/database/jobs_directory/000/121/upload_params.json' '142:/galaxy/server/database/objects/a/0/a/dataset_a0a5a363-dd65-4ec5-ad4d-8114b0ac97ed_files:/galaxy/server/database/objects/a/0/a/dataset_a0a5a363-dd65-4ec5-ad4d-8114b0ac97ed.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:15:15,268 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] (121) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/121/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/121/galaxy_121.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:15:22,871 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 121: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:15:27,398 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 121 finished +galaxy.model.metadata DEBUG 2024-09-14 01:15:27,451 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 142 +galaxy.jobs INFO 2024-09-14 01:15:27,487 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 121 in /galaxy/server/database/jobs_directory/000/121 +galaxy.jobs DEBUG 2024-09-14 01:15:27,534 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 121 executed (110.939 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:15:28,385 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 122 +tpv.core.entities DEBUG 2024-09-14 01:15:28,418 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/salmon/salmon/.*, abstract=False, cores=6, mem=70, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:15:28,418 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:15:28,423 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:15:28,437 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:15:28,454 [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 2024-09-14 01:15:28,461 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [122] queued (37.452 ms) +galaxy.jobs.handler INFO 2024-09-14 01:15:28,464 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (122) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:15:28,468 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 122 +galaxy.jobs DEBUG 2024-09-14 01:15:28,539 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [122] prepared (56.493 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:15:28,540 [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 2024-09-14 01:15:28,540 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1: mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:15:28,562 [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-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:15:28,586 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/122/tool_script.sh] for tool command [mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/a/0/a/dataset_a0a5a363-dd65-4ec5-ad4d-8114b0ac97ed.dat' && ln -s /galaxy/server/database/objects/a/0/a/dataset_a0a5a363-dd65-4ec5-ad4d-8114b0ac97ed.dat ./single.fasta && salmon quant --index './index' --libType U --unmatedReads ./single.fasta --threads "${GALAXY_SLOTS:-4}" --validateMappings --minScoreFraction '0.65' --ma '2' --mp '4' --go '5' --ge '3' --allowDovetail --recoverOrphans --incompatPrior '0.0' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '100' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '1e-05' -o ./output] +galaxy.jobs.runners DEBUG 2024-09-14 01:15:28,601 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (122) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; +if [ -f "/galaxy/server/database/jobs_directory/000/122/working/output/quant.sf" ] ; then cp "/galaxy/server/database/jobs_directory/000/122/working/output/quant.sf" "/galaxy/server/database/objects/6/2/e/dataset_62e35a26-421e-4fbb-a191-b44c2e9dcd92.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:15:28,614 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:15:28,614 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1: mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:15:28,633 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:15:34,095 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 122: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:15:38,851 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 122 finished +galaxy.model.metadata DEBUG 2024-09-14 01:15:38,953 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 143 +galaxy.util WARNING 2024-09-14 01:15:38,966 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Unable to honor primary group (grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=101, gr_mem=[])) for /galaxy/server/database/objects/6/2/e/dataset_62e35a26-421e-4fbb-a191-b44c2e9dcd92.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/6/2/e/dataset_62e35a26-421e-4fbb-a191-b44c2e9dcd92.dat' +galaxy.jobs INFO 2024-09-14 01:15:38,999 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Collecting metrics for Job 122 in /galaxy/server/database/jobs_directory/000/122 +galaxy.objectstore CRITICAL 2024-09-14 01:15:39,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] None delete error [Errno 13] Permission denied: 'cmd_info.json' +galaxy.jobs DEBUG 2024-09-14 01:15:39,037 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 122 executed (122.351 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:15:41,767 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 123 +tpv.core.entities DEBUG 2024-09-14 01:15:41,797 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:15:41,798 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:15:41,802 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:15:41,813 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:15:41,831 [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 2024-09-14 01:15:41,837 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [123] queued (35.380 ms) +galaxy.jobs.handler INFO 2024-09-14 01:15:41,841 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (123) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:15:41,845 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 123 +galaxy.jobs DEBUG 2024-09-14 01:15:41,944 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [123] prepared (84.228 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:15:41,964 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] 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' '144:/galaxy/server/database/objects/1/b/f/dataset_1bfa5e66-2410-430c-b76b-ad0f89c622cf_files:/galaxy/server/database/objects/1/b/f/dataset_1bfa5e66-2410-430c-b76b-ad0f89c622cf.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:15:41,977 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (123) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/123/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/123/galaxy_123.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:15:50,294 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 123: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:15:54,946 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 123 finished +galaxy.model.metadata DEBUG 2024-09-14 01:15:55,006 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 144 +galaxy.jobs INFO 2024-09-14 01:15:55,042 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 123 in /galaxy/server/database/jobs_directory/000/123 +galaxy.jobs DEBUG 2024-09-14 01:15:55,107 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 123 executed (132.160 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:15:56,120 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 124 +tpv.core.entities DEBUG 2024-09-14 01:15:56,157 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_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/salmon/salmon/.*, abstract=False, cores=6, mem=70, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:15:56,158 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:15:56,163 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:15:56,178 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:15:56,194 [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 2024-09-14 01:15:56,201 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [124] queued (38.258 ms) +galaxy.jobs.handler INFO 2024-09-14 01:15:56,205 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (124) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:15:56,210 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Starting queue_job for job 124 +galaxy.jobs DEBUG 2024-09-14 01:15:56,289 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Job wrapper for Job [124] prepared (60.060 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:15:56,290 [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 2024-09-14 01:15:56,290 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1: mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:15:56,312 [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-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:15:56,333 [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 [mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/1/b/f/dataset_1bfa5e66-2410-430c-b76b-ad0f89c622cf.dat' && ln -s /galaxy/server/database/objects/1/b/f/dataset_1bfa5e66-2410-430c-b76b-ad0f89c622cf.dat ./single.fasta && salmon quant --index './index' --libType U --unmatedReads ./single.fasta --threads "${GALAXY_SLOTS:-4}" --seqBias --gcBias --incompatPrior '0.0' --dumpEq --minAssignedFrags '10' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --initUniform --maxReadOcc '100' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --useEM --numGibbsSamples '0' --noGammaDraw --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '1e-05' -o ./output] +galaxy.jobs.runners DEBUG 2024-09-14 01:15:56,347 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] (124) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${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; +if [ -f "/galaxy/server/database/jobs_directory/000/124/working/output/quant.sf" ] ; then cp "/galaxy/server/database/jobs_directory/000/124/working/output/quant.sf" "/galaxy/server/database/objects/2/e/f/dataset_2ef95097-a72a-4d1f-9f2c-23c853c23b29.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:15:56,361 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:15:56,361 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1: mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:15:56,379 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-0fd299cadb7a80e2cc704b5d903ccc54893c512d:377fcafe3b6e7ef703094f8f47a64d081622ee09-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:16:01,507 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] executing external set_meta script for job 124: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:16:06,162 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 124 finished +galaxy.model.metadata DEBUG 2024-09-14 01:16:06,228 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 145 +galaxy.util WARNING 2024-09-14 01:16:06,235 [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/e/f/dataset_2ef95097-a72a-4d1f-9f2c-23c853c23b29.dat, group remains grp.struct_group(gr_name='nogroup', gr_passwd='x', gr_gid=65534, gr_mem=[]), error was: [Errno 1] Operation not permitted: '/galaxy/server/database/objects/2/e/f/dataset_2ef95097-a72a-4d1f-9f2c-23c853c23b29.dat' +galaxy.jobs INFO 2024-09-14 01:16:06,263 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] Collecting metrics for Job 124 in /galaxy/server/database/jobs_directory/000/124 +galaxy.objectstore CRITICAL 2024-09-14 01:16:06,298 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] None delete error [Errno 13] Permission denied: 'cmd_info.json' +galaxy.jobs DEBUG 2024-09-14 01:16:06,298 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 124 executed (104.883 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:16:10,492 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 126, 125 +tpv.core.entities DEBUG 2024-09-14 01:16:10,522 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:16:10,523 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:16:10,527 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:16:10,540 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:16:10,554 [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 2024-09-14 01:16:10,560 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [125] queued (32.959 ms) +galaxy.jobs.handler INFO 2024-09-14 01:16:10,563 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (125) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:16:10,568 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 125 +tpv.core.entities DEBUG 2024-09-14 01:16:10,576 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:16:10,577 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:16:10,582 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:16:10,598 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:16:10,627 [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 2024-09-14 01:16:10,635 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [126] queued (52.115 ms) +galaxy.jobs.handler INFO 2024-09-14 01:16:10,641 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (126) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:16:10,643 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Starting queue_job for job 126 +galaxy.jobs DEBUG 2024-09-14 01:16:10,690 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [125] prepared (101.398 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:16:10,717 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] 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' '146:/galaxy/server/database/objects/7/5/0/dataset_75030957-c55c-4285-b8e0-e34c7fe01ce7_files:/galaxy/server/database/objects/7/5/0/dataset_75030957-c55c-4285-b8e0-e34c7fe01ce7.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:16:10,728 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (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 $return_code" +galaxy.jobs DEBUG 2024-09-14 01:16:10,753 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Job wrapper for Job [126] prepared (89.581 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:16:10,773 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Built script [/galaxy/server/database/jobs_directory/000/126/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/126/registry.xml' '/galaxy/server/database/jobs_directory/000/126/upload_params.json' '147:/galaxy/server/database/objects/6/e/1/dataset_6e10fecc-c97b-4ca7-9da4-c40cc1d42723_files:/galaxy/server/database/objects/6/e/1/dataset_6e10fecc-c97b-4ca7-9da4-c40cc1d42723.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:16:10,785 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] (126) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/126/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/126/galaxy_126.ec; sh -c "exit $return_code" +galaxy.jobs.handler DEBUG 2024-09-14 01:16:11,644 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 127 +tpv.core.entities DEBUG 2024-09-14 01:16:11,678 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Ranking destinations: [runner=k8s, dest_name=k8s, min_accepted_cores=None, min_accepted_mem=None, min_accepted_gpus=None, max_accepted_cores=100, max_accepted_mem=800, max_accepted_gpus=None, tpv_dest_tags= tags=[], handler_tags=None id=k8s, abstract=False, cores=None, mem=None, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = 8, max_mem = 48, max_gpus = None, env=[], params={'docker_enabled': 'true', 'limits_cpu': '{cores}', 'limits_memory': '{mem}Gi', 'requests_cpu': '{cores}', 'requests_memory': '{mem}Gi'}, resubmit={}, tags= tags=[], rank=, inherits=None, context={}, rules={}] for entity: id=force_default_container_for_built_in_tools, Rule: force_default_container_for_built_in_tools, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true', 'docker_container_id_override': 'quay.io/galaxyproject/galaxy-anvil:23.1'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:16:11,678 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:16:11,683 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:16:11,699 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:16:11,715 [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 2024-09-14 01:16:11,720 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [127] queued (36.781 ms) +galaxy.jobs.handler INFO 2024-09-14 01:16:11,724 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (127) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:16:11,729 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 127 +galaxy.jobs DEBUG 2024-09-14 01:16:11,824 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [127] prepared (79.352 ms) +galaxy.jobs.command_factory INFO 2024-09-14 01:16:11,844 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/127/tool_script.sh] for tool command [python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/127/registry.xml' '/galaxy/server/database/jobs_directory/000/127/upload_params.json' '148:/galaxy/server/database/objects/4/a/4/dataset_4a48162c-a92c-4aa7-9e4c-28aae13d71e1_files:/galaxy/server/database/objects/4/a/4/dataset_4a48162c-a92c-4aa7-9e4c-28aae13d71e1.dat'] +galaxy.jobs.runners DEBUG 2024-09-14 01:16:11,857 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (127) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/127/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/127/galaxy_127.ec; sh -c "exit $return_code" +galaxy.jobs.runners DEBUG 2024-09-14 01:16:19,060 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] executing external set_meta script for job 125: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:16:19,082 [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 . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:16:20,430 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] executing external set_meta script for job 127: GALAXY_LIB="/galaxy/server/lib"; if [ "$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 2024-09-14 01:16:25,928 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] execution of external set_meta for job 125 finished +galaxy.model.metadata DEBUG 2024-09-14 01:16:26,017 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 146 +galaxy.jobs INFO 2024-09-14 01:16:26,056 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] Collecting metrics for Job 125 in /galaxy/server/database/jobs_directory/000/125 +galaxy.jobs.runners DEBUG 2024-09-14 01:16:26,070 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] execution of external set_meta for job 126 finished +galaxy.jobs DEBUG 2024-09-14 01:16:26,125 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-3] job_wrapper.finish for job 125 executed (166.222 ms) +galaxy.model.metadata DEBUG 2024-09-14 01:16:26,142 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] loading metadata from file for: HistoryDatasetAssociation 147 +galaxy.jobs INFO 2024-09-14 01:16:26,180 [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 DEBUG 2024-09-14 01:16:26,239 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-0] job_wrapper.finish for job 126 executed (144.291 ms) +galaxy.jobs.runners DEBUG 2024-09-14 01:16:26,964 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] execution of external set_meta for job 127 finished +galaxy.model.metadata DEBUG 2024-09-14 01:16:27,015 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] loading metadata from file for: HistoryDatasetAssociation 148 +galaxy.jobs INFO 2024-09-14 01:16:27,044 [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 2024-09-14 01:16:27,089 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] job_wrapper.finish for job 127 executed (99.360 ms) +galaxy.jobs.handler DEBUG 2024-09-14 01:16:28,260 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 128 +tpv.core.entities DEBUG 2024-09-14 01:16:28,303 [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=default, abstract=False, cores=1, mem=cores * 3.8, gpus=None, min_cores = None, min_mem = None, min_gpus = None, max_cores = None, max_mem = None, max_gpus = None, env=[], params={'container_monitor': False, 'docker_default_container_id': 'quay.io/galaxyproject/galaxy-anvil:23.1', 'tmp_dir': 'true'}, resubmit={}, tags= tags=[, ], rank=helpers.we, inherits=None, context={}, rules={} using custom function +galaxy.jobs.mapper DEBUG 2024-09-14 01:16:28,303 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Mapped job to destination id: k8s +galaxy.jobs.handler DEBUG 2024-09-14 01:16:28,308 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Dispatching to k8s runner +galaxy.jobs DEBUG 2024-09-14 01:16:28,324 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Persisting job destination (destination id: k8s) +galaxy.jobs DEBUG 2024-09-14 01:16:28,351 [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 2024-09-14 01:16:28,360 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] Job [128] queued (51.892 ms) +galaxy.jobs.handler INFO 2024-09-14 01:16:28,366 [pN:job_handler_0,p:8,tN:JobHandlerQueue.monitor_thread] (128) Job dispatched +galaxy.jobs.runners.kubernetes DEBUG 2024-09-14 01:16:28,368 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Starting queue_job for job 128 +galaxy.jobs DEBUG 2024-09-14 01:16:28,464 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Job wrapper for Job [128] prepared (78.237 ms) +galaxy.tool_util.deps.containers INFO 2024-09-14 01:16:28,464 [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 2024-09-14 01:16:28,465 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3: mulled-v2-373539cd51d908b0ef4294c9cff8015be7cf2072:242eaca4eb9c8ff4c9b6f90b393c876ccfa61003 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:16:28,637 [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-v2-373539cd51d908b0ef4294c9cff8015be7cf2072:242eaca4eb9c8ff4c9b6f90b393c876ccfa61003-0,type=docker]] +galaxy.jobs.command_factory INFO 2024-09-14 01:16:28,658 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Built script [/galaxy/server/database/jobs_directory/000/128/tool_script.sh] for tool command [ln -s /galaxy/server/database/objects/6/e/1/dataset_6e10fecc-c97b-4ca7-9da4-c40cc1d42723.dat reference.fa && ln -s /galaxy/server/database/objects/4/a/4/dataset_4a48162c-a92c-4aa7-9e4c-28aae13d71e1.dat query.fa && mummerplot -b '20' -s 'small' -terminal png -title 'Title' '/galaxy/server/database/objects/7/5/0/dataset_75030957-c55c-4285-b8e0-e34c7fe01ce7.dat' && gnuplot < out.gp] +galaxy.jobs.runners DEBUG 2024-09-14 01:16:28,721 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] (128) command is: mkdir -p working outputs configs +if [ -d _working ]; then + rm -rf working/ outputs/ configs/; cp -R _working working; cp -R _outputs outputs; cp -R _configs configs +else + cp -R working _working; cp -R outputs _outputs; cp -R configs _configs +fi +cd working; __out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$" +mkfifo "$__out" "$__err" +trap 'rm -f "$__out" "$__err"' EXIT +tee -a '../outputs/tool_stdout' < "$__out" & +tee -a '../outputs/tool_stderr' < "$__err" >&2 & /bin/bash /galaxy/server/database/jobs_directory/000/128/tool_script.sh > "$__out" 2> "$__err"; return_code=$?; echo $return_code > /galaxy/server/database/jobs_directory/000/128/galaxy_128.ec; +if [ -f "/galaxy/server/database/jobs_directory/000/128/working/out.gp" ] ; then cp "/galaxy/server/database/jobs_directory/000/128/working/out.gp" "/galaxy/server/database/objects/9/4/2/dataset_94263f6d-1ddc-405a-9095-6acd338bb982.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/128/working/out.fplot" ] ; then cp "/galaxy/server/database/jobs_directory/000/128/working/out.fplot" "/galaxy/server/database/objects/d/0/7/dataset_d0734c92-fe76-4825-92ed-ed4843743318.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/128/working/out.rplot" ] ; then cp "/galaxy/server/database/jobs_directory/000/128/working/out.rplot" "/galaxy/server/database/objects/6/1/9/dataset_6199b110-e8f3-4255-b15e-2a18875c43dc.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/128/working/out.hplot" ] ; then cp "/galaxy/server/database/jobs_directory/000/128/working/out.hplot" "/galaxy/server/database/objects/0/8/1/dataset_0816ce20-2b69-4ed0-acd4-29c3a99e3349.dat" ; fi; +if [ -f "/galaxy/server/database/jobs_directory/000/128/working/out.png" ] ; then cp "/galaxy/server/database/jobs_directory/000/128/working/out.png" "/galaxy/server/database/objects/3/6/c/dataset_36c0cffd-d993-4c16-8e58-f62a3e6731b2.dat" ; fi; sh -c "exit $return_code" +galaxy.tool_util.deps.containers INFO 2024-09-14 01:16:28,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [ExplicitContainerResolver[]] found description [None] +galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2024-09-14 01:16:28,734 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3: mulled-v2-373539cd51d908b0ef4294c9cff8015be7cf2072:242eaca4eb9c8ff4c9b6f90b393c876ccfa61003 +galaxy.tool_util.deps.containers INFO 2024-09-14 01:16:28,752 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/mulled-v2-373539cd51d908b0ef4294c9cff8015be7cf2072:242eaca4eb9c8ff4c9b6f90b393c876ccfa61003-0,type=docker]] +galaxy.jobs.runners DEBUG 2024-09-14 01:16:54,832 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] executing external set_meta script for job 128: GALAXY_LIB="/galaxy/server/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="None"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python metadata/set.py +galaxy.jobs.runners DEBUG 2024-09-14 01:16:59,547 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] execution of external set_meta for job 128 finished +galaxy.model.metadata DEBUG 2024-09-14 01:16:59,602 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 149 +galaxy.model.metadata DEBUG 2024-09-14 01:16:59,613 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 150 +galaxy.model.metadata DEBUG 2024-09-14 01:16:59,624 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 151 +galaxy.model.metadata DEBUG 2024-09-14 01:16:59,635 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 152 +galaxy.model.metadata DEBUG 2024-09-14 01:16:59,645 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] loading metadata from file for: HistoryDatasetAssociation 153 +galaxy.jobs INFO 2024-09-14 01:16:59,686 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] Collecting metrics for Job 128 in /galaxy/server/database/jobs_directory/000/128 +galaxy.jobs DEBUG 2024-09-14 01:16:59,748 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-2] job_wrapper.finish for job 128 executed (172.546 ms) diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/jobs.txt b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/jobs.txt new file mode 100644 index 000000000..152a33633 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/jobs.txt @@ -0,0 +1,128 @@ +b7c0a16325039497 ok 2024-09-14T01:16:59.690383 toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3 +2cd1d76bf2ef465f ok 2024-09-14T01:16:27.046639 upload1 +8ebbb1e4f11076af ok 2024-09-14T01:16:26.183377 upload1 +234c1bcaae2914ca ok 2024-09-14T01:16:26.059403 upload1 +9a28a94cdc902f04 ok 2024-09-14T01:16:06.267378 toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1 +54fc498ddf93b220 ok 2024-09-14T01:15:55.046025 upload1 +765d4069e7f77bff ok 2024-09-14T01:15:39.003440 toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1 +cfa693d8e6b4174a ok 2024-09-14T01:15:27.490562 upload1 +52d5cbcb026d8518 ok 2024-09-14T01:15:11.675578 toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1 +fa3f703e66538a8e ok 2024-09-14T01:14:58.285292 upload1 +066a24ce2001c2a8 ok 2024-09-14T01:14:57.400617 upload1 +7f019bb254bd9239 ok 2024-09-14T01:14:39.710818 toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1 +c51f3c4644daf9a5 ok 2024-09-14T01:14:27.368652 upload1 +38d82a18eaba87f9 ok 2024-09-14T01:14:12.314272 toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1 +03016dc1802ebe2b ok 2024-09-14T01:13:59.232954 upload1 +bd5e06df4cb7f9fc ok 2024-09-14T01:13:43.159739 toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1 +a5bab748014374bb ok 2024-09-14T01:13:15.307716 upload1 +22470166765b2f95 ok 2024-09-14T01:12:59.097096 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0 +251b4eb87d395ff4 ok 2024-09-14T01:12:47.775767 upload1 +ffe3188988274058 ok 2024-09-14T01:12:32.874760 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0 +2ca487e824fa2a6a ok 2024-09-14T01:12:22.692886 upload1 +4c4c4e06aa36dd6f ok 2024-09-14T01:12:06.394117 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0 +6866e8eee2e30678 ok 2024-09-14T01:11:50.181251 upload1 +fb28fb836c18096d ok 2024-09-14T01:11:32.013434 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0 +cbd23c4cd10aa88a ok 2024-09-14T01:11:19.748732 upload1 +4f3352db0d5bc390 error 2024-09-14T01:11:04.701248 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0 +cc384397a197f1fe ok 2024-09-14T01:10:56.958423 upload1 +4807d53d9a2e2e7f ok 2024-09-14T01:10:39.819748 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0 +45622d042ca95d2d ok 2024-09-14T01:10:27.380659 upload1 +34c46068446c92bb ok 2024-09-14T01:10:11.004685 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0 +9286c7c1ce47fbe4 ok 2024-09-14T01:09:42.575391 upload1 +022a03c7fd9fc863 ok 2024-09-14T01:09:25.677885 toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1 +b914c5cbdc32f1b4 ok 2024-09-14T01:09:12.559307 upload1 +50976ab105970f33 ok 2024-09-14T01:08:56.406003 toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1 +153dc00d25d9a6d7 ok 2024-09-14T01:08:20.442108 upload1 +fb8ab536889f0e94 ok 2024-09-14T01:08:03.049451 toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0 +748366871c7f2141 ok 2024-09-14T01:07:51.878852 upload1 +d58abde2fb36f1e8 ok 2024-09-14T01:07:34.540977 toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0 +c9147cfbb24d024f ok 2024-09-14T01:07:23.347593 upload1 +e5e85752534a1f6b ok 2024-09-14T01:07:07.133859 toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0 +6872c13e0305d080 ok 2024-09-14T01:06:52.877548 upload1 +f513f03dee6ba111 error 2024-09-14T01:06:36.828805 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5 +1747158b9458f9f7 ok 2024-09-14T01:06:30.596914 upload1 +0ac6b3678845426c ok 2024-09-14T01:06:29.647173 upload1 +16a1aab48891616f ok 2024-09-14T01:06:13.822806 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5 +1913c0b28f54e065 ok 2024-09-14T01:06:02.847899 upload1 +050fdb9488518af8 ok 2024-09-14T01:05:46.323294 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5 +5c0d3387021faa81 ok 2024-09-14T01:05:35.362237 upload1 +0dd086a5fc3869bf ok 2024-09-14T01:05:18.846615 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5 +6392c2499aa3e408 ok 2024-09-14T01:05:07.922888 upload1 +d49c36adeba8557f ok 2024-09-14T01:05:07.879357 upload1 +b94e2d0d46c75809 ok 2024-09-14T01:04:51.055051 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5 +b355a78f591d3088 ok 2024-09-14T01:04:41.165010 upload1 +dc1abf31b7878b39 ok 2024-09-14T01:04:40.415244 upload1 +2611c7230f4ebe6d ok 2024-09-14T01:04:23.468081 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5 +c12cff306b1f27cd ok 2024-09-14T01:04:10.922790 upload1 +2c20b2126db3a04f ok 2024-09-14T01:04:10.159783 upload1 +fa93e67c1e1ebcf1 ok 2024-09-14T01:04:09.227682 upload1 +4b3b265db2b6345e error 2024-09-14T01:03:51.267360 upload1 +87dadb2c71819a0b ok 2024-09-14T01:03:40.166985 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5 +ab33a4ba552f72dc ok 2024-09-14T01:03:28.170179 upload1 +1a9d1a58818c88c1 ok 2024-09-14T01:03:09.563688 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4 +548270c1cda12d7a ok 2024-09-14T01:02:58.324835 upload1 +5138b028115a7f5f ok 2024-09-14T01:02:43.260801 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4 +6ec8bf3c5dc3224e ok 2024-09-14T01:02:27.921757 upload1 +24e58a97d82a5b14 ok 2024-09-14T01:02:11.867407 toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2 +54816788543a0d5a ok 2024-09-14T01:02:00.778153 upload1 +1e7e26c0720680d3 ok 2024-09-14T01:01:59.773023 upload1 +1762d3613701af86 ok 2024-09-14T01:01:43.176875 toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2 +9cbc3100f8d963dc ok 2024-09-14T01:01:32.320841 upload1 +58bcb7304f57378f ok 2024-09-14T01:01:30.223043 upload1 +95a0a0882149fa40 ok 2024-09-14T01:01:15.342757 toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2 +5df7adb272208d2d ok 2024-09-14T01:00:58.297240 upload1 +2ea84bc3d4af7b79 ok 2024-09-14T01:00:58.207321 upload1 +219eea5edfdc4ae8 error 2024-09-14T01:00:45.403522 upload1 +0aec0cc69095fb2b error 2024-09-14T01:00:42.626264 upload1 +4fe3ac1409aa61b5 ok 2024-09-14T01:00:31.820285 toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9 +d0d1c4024af98dfb ok 2024-09-14T01:00:21.746412 upload1 +517cff8f48d5d3c0 ok 2024-09-14T01:00:06.510190 toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9 +9184366d0e5e1098 ok 2024-09-14T00:59:55.942650 upload1 +169d16a8c5164f68 ok 2024-09-14T00:59:40.743351 toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9 +9907fa81e6c94704 ok 2024-09-14T00:59:30.680339 upload1 +50872bd7722d341d ok 2024-09-14T00:59:14.412945 toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9 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2024-09-14T00:54:19.702304 toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 +4a12ddb120e74961 ok 2024-09-14T00:54:08.596910 upload1 +c0c8a69c8070f677 ok 2024-09-14T00:54:08.442187 upload1 +7bf7e48be40dc04d ok 2024-09-14T00:53:50.215090 toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 +0c8c289d788b4c08 ok 2024-09-14T00:53:38.810018 upload1 +defb5211a6a94aa8 ok 2024-09-14T00:53:37.694598 upload1 +fe0a9ea15b54bf6c error 2024-09-14T00:53:23.031439 upload1 +a57289ad4f175228 ok 2024-09-14T00:53:10.791471 toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 +49702c00cc3a3629 ok 2024-09-14T00:52:45.147767 upload1 +3ec05b8c179927a5 ok 2024-09-14T00:52:27.913078 toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.8+galaxy0 +24323ccc9ba4a0ff ok 2024-09-14T00:52:14.603990 upload1 +a66ef6e4a4a0e1d4 ok 2024-09-14T00:51:58.195084 toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1 +f560f43330980975 ok 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beta.kubernetes.io/instance-type=e2-custom-20-81920 + beta.kubernetes.io/os=linux + cloud.google.com/gke-boot-disk=pd-balanced + cloud.google.com/gke-container-runtime=containerd + cloud.google.com/gke-cpu-scaling-level=20 + cloud.google.com/gke-logging-variant=DEFAULT + cloud.google.com/gke-max-pods-per-node=110 + cloud.google.com/gke-nodepool=default-pool + cloud.google.com/gke-os-distribution=cos + cloud.google.com/gke-provisioning=standard + cloud.google.com/gke-stack-type=IPV4 + cloud.google.com/machine-family=e2 + cloud.google.com/private-node=false + failure-domain.beta.kubernetes.io/region=us-east1 + failure-domain.beta.kubernetes.io/zone=us-east1-b + kubernetes.io/arch=amd64 + kubernetes.io/hostname=gke-prod-24-09-14-00-32-default-pool-474c8ada-drxd + 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: 7137913088409953528 + csi.volume.kubernetes.io/nodeid: + {"cvmfs.csi.cern.ch":"gke-prod-24-09-14-00-32-default-pool-474c8ada-drxd","pd.csi.storage.gke.io":"projects/anvil-and-terra-development/zo... + node.alpha.kubernetes.io/ttl: 0 + node.gke.io/last-applied-node-labels: + cloud.google.com/gke-boot-disk=pd-balanced,cloud.google.com/gke-container-runtime=containerd,cloud.google.com/gke-cpu-scaling-level=20,clo... + node.gke.io/last-applied-node-taints: + volumes.kubernetes.io/controller-managed-attach-detach: true +CreationTimestamp: Sat, 14 Sep 2024 00:38:48 +0000 +Taints: +Unschedulable: false +Lease: + HolderIdentity: gke-prod-24-09-14-00-32-default-pool-474c8ada-drxd + AcquireTime: + RenewTime: Sat, 14 Sep 2024 01:17:49 +0000 +Conditions: + Type Status LastHeartbeatTime LastTransitionTime Reason Message + ---- ------ ----------------- ------------------ ------ ------- + DeprecatedPullingSchemaV1Image False Sat, 14 Sep 2024 01:13:52 +0000 Sat, 14 Sep 2024 00:38:48 +0000 DeprecatedPullingSchemaV1ImageDetected No deprecation risk: did not pull any schema v1 images + DeprecatedUsingV1Alpha2Cri False Sat, 14 Sep 2024 01:13:52 +0000 Sat, 14 Sep 2024 00:38:48 +0000 DeprecatedUsingV1Alpha2CriNotDetected No deprecation risk: did not use v1alpha2 CRI + DeprecatedConfigsFieldInContainerdConfiguration False Sat, 14 Sep 2024 01:13:52 +0000 Sat, 14 Sep 2024 00:38:48 +0000 DeprecatedConfigsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'configs' field in containerd's config + DeprecatedMirrorsFieldInContainerdConfiguration False Sat, 14 Sep 2024 01:13:52 +0000 Sat, 14 Sep 2024 00:38:48 +0000 DeprecatedMirrorsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'mirrors' field in containerd's config + DeprecatedAuthsFieldInContainerdConfiguration False Sat, 14 Sep 2024 01:13:52 +0000 Sat, 14 Sep 2024 00:38:48 +0000 DeprecatedAuthsFieldInContainerdConfigurationNotDetected No deprecation risk: did not find any deprecated 'auths' field in containerd's config + DeprecatedOtherContainerdFeatures False Sat, 14 Sep 2024 01:13:52 +0000 Sat, 14 Sep 2024 00:38:48 +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. + CorruptDockerOverlay2 False Sat, 14 Sep 2024 01:13:52 +0000 Sat, 14 Sep 2024 00:38:48 +0000 NoCorruptDockerOverlay2 docker overlay2 is functioning properly + KernelDeadlock False Sat, 14 Sep 2024 01:13:52 +0000 Sat, 14 Sep 2024 00:38:48 +0000 KernelHasNoDeadlock kernel has no deadlock + FrequentContainerdRestart False Sat, 14 Sep 2024 01:13:52 +0000 Sat, 14 Sep 2024 00:38:48 +0000 NoFrequentContainerdRestart containerd is functioning properly + FrequentKubeletRestart False Sat, 14 Sep 2024 01:13:52 +0000 Sat, 14 Sep 2024 00:38:48 +0000 NoFrequentKubeletRestart kubelet is functioning properly + FrequentDockerRestart False Sat, 14 Sep 2024 01:13:52 +0000 Sat, 14 Sep 2024 00:38:48 +0000 NoFrequentDockerRestart docker is functioning properly + SysctlChanged False Sat, 14 Sep 2024 01:13:52 +0000 Sat, 14 Sep 2024 00:38:48 +0000 SysctlNotChanged Default sysctls are in effect, no unexpected sysctl changes + FrequentUnregisterNetDevice False Sat, 14 Sep 2024 01:13:52 +0000 Sat, 14 Sep 2024 00:38:48 +0000 NoFrequentUnregisterNetDevice node is functioning properly + ReadonlyFilesystem False Sat, 14 Sep 2024 01:13:52 +0000 Sat, 14 Sep 2024 00:38:48 +0000 FilesystemIsNotReadOnly Filesystem is not read-only + NetworkUnavailable False Sat, 14 Sep 2024 00:38:49 +0000 Sat, 14 Sep 2024 00:38:48 +0000 RouteCreated NodeController create implicit route + MemoryPressure False Sat, 14 Sep 2024 01:17:04 +0000 Sat, 14 Sep 2024 00:38:42 +0000 KubeletHasSufficientMemory kubelet has sufficient memory available + DiskPressure False Sat, 14 Sep 2024 01:17:04 +0000 Sat, 14 Sep 2024 00:38:42 +0000 KubeletHasNoDiskPressure kubelet has no disk pressure + PIDPressure False Sat, 14 Sep 2024 01:17:04 +0000 Sat, 14 Sep 2024 00:38:42 +0000 KubeletHasSufficientPID kubelet has sufficient PID available + Ready True Sat, 14 Sep 2024 01:17:04 +0000 Sat, 14 Sep 2024 00:39:08 +0000 KubeletReady kubelet is posting ready status. AppArmor enabled +Addresses: + InternalIP: 10.142.15.215 + ExternalIP: 34.74.38.98 + Hostname: gke-prod-24-09-14-00-32-default-pool-474c8ada-drxd +Capacity: + cpu: 20 + ephemeral-storage: 98831908Ki + hugepages-1Gi: 0 + hugepages-2Mi: 0 + memory: 82369080Ki + pods: 110 +Allocatable: + cpu: 19880m + ephemeral-storage: 47060071478 + hugepages-1Gi: 0 + hugepages-2Mi: 0 + memory: 75554360Ki + pods: 110 +System Info: + Machine ID: 864347bb08f3d7b8cffd6f1c6fda3639 + System UUID: 864347bb-08f3-d7b8-cffd-6f1c6fda3639 + Boot ID: 2092f847-188a-4385-8bf4-81d7b50c1fdc + Kernel Version: 6.1.85+ + OS Image: Container-Optimized OS from Google + Operating System: linux + Architecture: amd64 + Container Runtime Version: containerd://1.7.15 + Kubelet Version: v1.28.12-gke.1052000 + Kube-Proxy Version: v1.28.12-gke.1052000 +PodCIDR: 10.96.0.0/24 +PodCIDRs: 10.96.0.0/24 +ProviderID: gce://anvil-and-terra-development/us-east1-b/gke-prod-24-09-14-00-32-default-pool-474c8ada-drxd +Non-terminated Pods: (26 in total) + Namespace Name CPU Requests CPU Limits Memory Requests Memory Limits Age + --------- ---- ------------ ---------- --------------- ------------- --- + gmp-system collector-xpw5w 5m (0%) 0 (0%) 36M (0%) 3032M (3%) 38m + gmp-system gmp-operator-5c96f94977-79ww2 1m (0%) 0 (0%) 16M (0%) 2G (2%) 39m + kube-system event-exporter-gke-58c99c7869-2q69z 3m (0%) 0 (0%) 100Mi (0%) 0 (0%) 39m + kube-system fluentbit-gke-lnkgc 100m (0%) 0 (0%) 200Mi (0%) 500Mi (0%) 39m + kube-system gke-metrics-agent-dbzcp 9m (0%) 0 (0%) 110Mi (0%) 110Mi (0%) 39m + kube-system konnectivity-agent-autoscaler-697695f8c5-wqstt 10m (0%) 0 (0%) 10M (0%) 0 (0%) 39m + kube-system konnectivity-agent-bff86cf6b-gqlg7 15m (0%) 0 (0%) 60Mi (0%) 155Mi (0%) 39m + kube-system kube-dns-6f955b858b-5cbvh 260m (1%) 0 (0%) 110Mi (0%) 210Mi (0%) 40m + kube-system kube-dns-autoscaler-755c7dfdf5-txqpv 20m (0%) 0 (0%) 10Mi (0%) 0 (0%) 40m + kube-system kube-proxy-gke-prod-24-09-14-00-32-default-pool-474c8ada-drxd 100m (0%) 0 (0%) 0 (0%) 0 (0%) 38m + kube-system l7-default-backend-85b45d5c78-pzs2z 10m (0%) 0 (0%) 20Mi (0%) 0 (0%) 39m + kube-system metrics-server-v0.7.0-7787fd6556-gjdvk 48m (0%) 43m (0%) 105Mi (0%) 355Mi (0%) 38m + kube-system pdcsi-node-bmf68 10m (0%) 0 (0%) 20Mi (0%) 100Mi (0%) 39m + prod-24-09-14-00-32-1 prod-24-09-14-00-32-1-cvmfscsi-controllerplugin-84c648c6c78hxc6 0 (0%) 0 (0%) 0 (0%) 0 (0%) 36m + prod-24-09-14-00-32-1 prod-24-09-14-00-32-1-cvmfscsi-nodeplugin-z5ddh 0 (0%) 0 (0%) 0 (0%) 0 (0%) 31m + prod-24-09-14-00-32-1 prod-24-09-14-00-32-1-galaxy-celery-6879d77764-jt7hn 500m (2%) 2 (10%) 2G (2%) 8G (10%) 36m + prod-24-09-14-00-32-1 prod-24-09-14-00-32-1-galaxy-celery-beat-896475fd7-z86ss 500m (2%) 2 (10%) 2G (2%) 8G (10%) 36m + prod-24-09-14-00-32-1 prod-24-09-14-00-32-1-galaxy-galaxy-postgres-0 250m (1%) 0 (0%) 256Mi (0%) 0 (0%) 36m + prod-24-09-14-00-32-1 prod-24-09-14-00-32-1-galaxy-job-0-6997df587f-q7l69 500m (2%) 2 (10%) 2G (2%) 8G (10%) 36m + prod-24-09-14-00-32-1 prod-24-09-14-00-32-1-galaxy-nginx-7b7b4d7b4d-s7kpk 100m (0%) 2 (10%) 500M (0%) 3G (3%) 36m + prod-24-09-14-00-32-1 prod-24-09-14-00-32-1-galaxy-rabbitmq-server-server-0 1 (5%) 2 (10%) 2Gi (2%) 2Gi (2%) 36m + prod-24-09-14-00-32-1 prod-24-09-14-00-32-1-galaxy-web-5b6d5ff49f-j7gh9 500m (2%) 2 (10%) 2G (2%) 8G (10%) 36m + prod-24-09-14-00-32-1 prod-24-09-14-00-32-1-galaxy-workflow-5bbc9bd54f-m5vvv 500m (2%) 2 (10%) 2G (2%) 8G (10%) 36m + prod-24-09-14-00-32-1 prod-24-09-14-00-32-1-nfs-0 0 (0%) 0 (0%) 0 (0%) 0 (0%) 36m + prod-24-09-14-00-32-1 prod-24-09-14-00-32-1-rabbitmq-56b96b8964-smd8k 0 (0%) 0 (0%) 0 (0%) 0 (0%) 36m + prod-24-09-14-00-32-1 prod-24-09-14-00-32-1-rabbitmq-messaging-topology-operatorkgchh 0 (0%) 0 (0%) 0 (0%) 0 (0%) 36m +Allocated resources: + (Total limits may be over 100 percent, i.e., overcommitted.) + Resource Requests Limits + -------- -------- ------ + cpu 4441m (22%) 14043m (70%) + memory 13748622464 (17%) 51678947328 (66%) + ephemeral-storage 35Gi (79%) 200Gi (456%) + hugepages-1Gi 0 (0%) 0 (0%) + hugepages-2Mi 0 (0%) 0 (0%) +Events: + Type Reason Age From Message + ---- ------ ---- ---- ------- + Normal Starting 39m kube-proxy + Normal Starting 42m kubelet Starting kubelet. + Warning InvalidDiskCapacity 42m kubelet invalid capacity 0 on image filesystem + Normal NodeAllocatableEnforced 42m kubelet Updated Node Allocatable limit across pods + Normal NodeHasNoDiskPressure 40m (x7 over 42m) kubelet Node gke-prod-24-09-14-00-32-default-pool-474c8ada-drxd status is now: NodeHasNoDiskPressure + Normal NodeHasSufficientPID 40m (x7 over 42m) kubelet Node gke-prod-24-09-14-00-32-default-pool-474c8ada-drxd status is now: NodeHasSufficientPID + Normal NodeHasSufficientMemory 40m (x8 over 42m) kubelet Node gke-prod-24-09-14-00-32-default-pool-474c8ada-drxd status is now: NodeHasSufficientMemory + Warning NodeRegistrationCheckerStart 39m node-registration-checker-monitor Sat Sep 14 00:34:56 UTC 2024 - ** Starting Node Registration Checker ** + Normal Synced 39m cloud-node-controller Node synced successfully + Normal RegisteredNode 39m node-controller Node gke-prod-24-09-14-00-32-default-pool-474c8ada-drxd event: Registered Node gke-prod-24-09-14-00-32-default-pool-474c8ada-drxd in Controller + Warning NodeRegistrationCheckerDidNotRunChecks 35m node-registration-checker-monitor Sat Sep 14 00:41:56 UTC 2024 - ** Node ready and registered. ** diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/results.html b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/results.html new file mode 100644 index 000000000..1db6d6596 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/results.html @@ -0,0 +1,291 @@ + + + + + + + Test Results (powered by Planemo) + + + + + + + + + + +
+
+
+
+ + + + + + + \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/results.json b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/results.json new file mode 100644 index 000000000..db97701f2 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 59, "errors": 6, "failures": 5, "skips": 2}, "tests": [{"id": "annotatemyids/3.5.0.1-0", "has_data": true, "data": {"tool_id": "annotatemyids", "tool_version": "3.5.0.1", "test_index": 0, "time_seconds": 95.3273241519928, "inputs": {"id_file": {"src": "hda", "id": "ed165837e8ba4cca"}, "organism": "Hs", "id_type": "SYMBOL"}, "job": {"model_class": "Job", "id": "a21c742fb7f71c24", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T00:49:43.624935", "create_time": "2024-09-14T00:48:37.348132", "galaxy_version": "23.1", "command_version": "R version 3.4.1 (2017-06-30) -- \"Single Candle\", org.Hs.eg.db version 3.5.0, org.Dr.eg.db version 3.5.0, org.Dm.eg.db version 3.5.0, org.Mm.eg.db version 3.5.0", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-slmhz", "command_line": "Rscript '/galaxy/server/database/jobs_directory/000/2/configs/tmpjmea5ee0'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "rscriptOpt": "false", "remove_dups": "false", "output_cols": "[\"ENSEMBL\", \"ENTREZID\", \"SYMBOL\", \"GENENAME\"]", "id_type": "\"SYMBOL\"", "organism": "\"Hs\"", "file_has_header": "false"}, "inputs": {"id_file": {"id": "ed165837e8ba4cca", "src": "hda", "uuid": "b41ebb76-86b4-41cb-a3e8-cbb5c2c57aa9"}}, "outputs": {"out_tab": {"id": "a21c742fb7f71c24", "src": "hda", "uuid": "cf22f82f-58d6-4bfd-b627-847a3e88c616"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:1 mapping between keys and columns\n", "job_stdout": "", "job_stderr": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:1 mapping between keys and columns\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "17 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "17.0000000"}, {"title": "Job End Time", "value": "2024-09-14 00:49:33", "plugin": "core", "name": "end_epoch", "raw_value": "1726274973.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 00:49:16", "plugin": "core", "name": "start_epoch", "raw_value": "1726274956.0000000"}, {"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": "annotatemyids/3.5.0.1-1", "has_data": true, "data": {"tool_id": "annotatemyids", "tool_version": "3.5.0.1", "test_index": 1, "time_seconds": 44.71670174598694, "inputs": {"id_file": {"src": "hda", "id": "198a4099c8492732"}, "organism": "Hs", "id_type": "ENSEMBL", "rscriptOpt": true}, "job": {"model_class": "Job", "id": "ef71afcbd5eac7e6", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T00:50:28.052753", "create_time": "2024-09-14T00:50:00.443420", "galaxy_version": "23.1", "command_version": "R version 3.4.1 (2017-06-30) -- \"Single Candle\", org.Hs.eg.db version 3.5.0, org.Dr.eg.db version 3.5.0, org.Dm.eg.db version 3.5.0, org.Mm.eg.db version 3.5.0", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-qv754", "command_line": "cp '/galaxy/server/database/jobs_directory/000/4/configs/tmpq4rl6ibw' '/galaxy/server/database/objects/1/f/8/dataset_1f8473b4-9443-4cd9-b93f-067b4d68c220.dat' && Rscript '/galaxy/server/database/jobs_directory/000/4/configs/tmpq4rl6ibw'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "rscriptOpt": "true", "remove_dups": "false", "output_cols": "[\"ENSEMBL\", \"ENTREZID\", \"SYMBOL\", \"GENENAME\"]", "id_type": "\"ENSEMBL\"", "organism": "\"Hs\"", "file_has_header": "false"}, "inputs": {"id_file": {"id": "198a4099c8492732", "src": "hda", "uuid": "73070225-33dc-4d2f-a4bb-7f6d73dd3d01"}}, "outputs": {"out_rscript": {"id": "e39ca091cf5339f4", "src": "hda", "uuid": "1f8473b4-9443-4cd9-b93f-067b4d68c220"}, "out_tab": {"id": "ef71afcbd5eac7e6", "src": "hda", "uuid": "335bb676-a9f6-4c88-a6d2-298699f8890a"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:1 mapping between keys and columns\n", "job_stdout": "", "job_stderr": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:1 mapping between keys and columns\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "17 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "17.0000000"}, {"title": "Job End Time", "value": "2024-09-14 00:50:19", "plugin": "core", "name": "end_epoch", "raw_value": "1726275019.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 00:50:02", "plugin": "core", "name": "start_epoch", "raw_value": "1726275002.0000000"}, {"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": "annotatemyids/3.5.0.1-2", "has_data": true, "data": {"tool_id": "annotatemyids", "tool_version": "3.5.0.1", "test_index": 2, "time_seconds": 44.48130512237549, "inputs": {"id_file": {"src": "hda", "id": "cf4669e3d1f60b4e"}, "organism": "Hs", "id_type": "ENSEMBL", "output_cols": ["ENSEMBL", "GO", "ONTOLOGY", "EVIDENCE"]}, "job": {"model_class": "Job", "id": "cf4669e3d1f60b4e", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T00:51:13.500420", "create_time": "2024-09-14T00:50:45.645965", "galaxy_version": "23.1", "command_version": "R version 3.4.1 (2017-06-30) -- \"Single Candle\", org.Hs.eg.db version 3.5.0, org.Dr.eg.db version 3.5.0, org.Dm.eg.db version 3.5.0, org.Mm.eg.db version 3.5.0", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-2qmrp", "command_line": "Rscript '/galaxy/server/database/jobs_directory/000/6/configs/tmpuk790mlu'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "rscriptOpt": "false", "remove_dups": "false", "output_cols": "[\"ENSEMBL\", \"GO\", \"ONTOLOGY\", \"EVIDENCE\"]", "id_type": "\"ENSEMBL\"", "organism": "\"Hs\"", "file_has_header": "false"}, "inputs": {"id_file": {"id": "cf4669e3d1f60b4e", "src": "hda", "uuid": "fe681ec1-6341-4ff3-91be-67bab7337de5"}}, "outputs": {"out_tab": {"id": "f560f43330980975", "src": "hda", "uuid": "21c89c91-f995-459e-b47e-d2e33ae3547e"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:many mapping between keys and columns\n", "job_stdout": "", "job_stderr": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:many mapping between keys and columns\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "18 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "18.0000000"}, {"title": "Job End Time", "value": "2024-09-14 00:51:05", "plugin": "core", "name": "end_epoch", "raw_value": "1726275065.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 00:50:47", "plugin": "core", "name": "start_epoch", "raw_value": "1726275047.0000000"}, {"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": "annotatemyids/3.5.0.1-3", "has_data": true, "data": {"tool_id": "annotatemyids", "tool_version": "3.5.0.1", "test_index": 3, "time_seconds": 44.846510887145996, "inputs": {"id_file": {"src": "hda", "id": "a66ef6e4a4a0e1d4"}, "organism": "Hs", "id_type": "ENSEMBL", "output_cols": ["ENSEMBL", "GO", "ONTOLOGY", "EVIDENCE"], "remove_dups": true}, "job": {"model_class": "Job", "id": "a66ef6e4a4a0e1d4", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T00:51:58.195084", "create_time": "2024-09-14T00:51:30.233198", "galaxy_version": "23.1", "command_version": "R version 3.4.1 (2017-06-30) -- \"Single Candle\", org.Hs.eg.db version 3.5.0, org.Dr.eg.db version 3.5.0, org.Dm.eg.db version 3.5.0, org.Mm.eg.db version 3.5.0", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-8zbmk", "command_line": "Rscript '/galaxy/server/database/jobs_directory/000/8/configs/tmpfbw71315'", "traceback": null, "params": {"file_has_header": "false", "organism": "\"Hs\"", "id_type": "\"ENSEMBL\"", "output_cols": "[\"ENSEMBL\", \"GO\", \"ONTOLOGY\", \"EVIDENCE\"]", "remove_dups": "true", "rscriptOpt": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"tabular\""}, "inputs": {"id_file": {"id": "a66ef6e4a4a0e1d4", "src": "hda", "uuid": "594ce8d3-34d3-4e83-ba57-7f6cd4a922d3"}}, "outputs": {"out_tab": {"id": "24323ccc9ba4a0ff", "src": "hda", "uuid": "16f94c91-8c43-4524-988d-4e562228ca48"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:many mapping between keys and columns\n", "job_stdout": "", "job_stderr": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:many mapping between keys and columns\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "18 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "18.0000000"}, {"title": "Job End Time", "value": "2024-09-14 00:51:49", "plugin": "core", "name": "end_epoch", "raw_value": "1726275109.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 00:51:31", "plugin": "core", "name": "start_epoch", "raw_value": "1726275091.0000000"}, {"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_call/1.15.1+galaxy5-0", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 0, "time_seconds": 29.13078284263611, "inputs": {"input_file": {"src": "hda", "id": "1747158b9458f9f7"}, "sec_consensus_variant_calling|variant_calling|method": "multiallelic", "sec_input_output|variants_only": true, "output_type": "v"}, "job": {"model_class": "Job", "id": "87dadb2c71819a0b", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:03:40.166985", "create_time": "2024-09-14T01:03:28.617553", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "history_id": "ed165837e8ba4cca", "external_id": "gxy-fdrzc", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/9/0/b/dataset_90bc8cb7-14e1-41de-b44e-84736db0e809.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --variants-only --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/2/d/3/dataset_2d3b832f-33d5-42d1-8517-9fffd277ea4e.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": false, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": null, \"skip_variants\": null, \"variants_only\": true}", "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 0, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}, \"gvcf\": \"\", \"method\": \"multiallelic\", \"prior\": \"0.0011\", \"prior_freqs\": \"\"}}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}"}, "inputs": {"input_file": {"id": "1747158b9458f9f7", "src": "hda", "uuid": "90bc8cb7-14e1-41de-b44e-84736db0e809"}}, "outputs": {"output_file": {"id": "f513f03dee6ba111", "src": "hda", "uuid": "2d3b832f-33d5-42d1-8517-9fffd277ea4e"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n", "job_stdout": "", "job_stderr": "", "stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-14 01:03:31", "plugin": "core", "name": "end_epoch", "raw_value": "1726275811.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:03:30", "plugin": "core", "name": "start_epoch", "raw_value": "1726275810.0000000"}, {"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_call/1.15.1+galaxy5-1", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 1, "time_seconds": 10.503514289855957, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_call/1.15.1+galaxy5-2", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 2, "time_seconds": 32.821192502975464, "inputs": {"input_file": {"src": "hda", "id": "e5e85752534a1f6b"}, "sec_restrict|samples_file": {"src": "hda", "id": "c9147cfbb24d024f"}, "sec_consensus_variant_calling|variant_calling|method": "multiallelic", "sec_file_format|ploidy_file": {"src": "hda", "id": "d58abde2fb36f1e8"}, "output_type": "v"}, "job": {"model_class": "Job", "id": "2611c7230f4ebe6d", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:04:23.468081", "create_time": "2024-09-14T01:04:11.245672", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "history_id": "ed165837e8ba4cca", "external_id": "gxy-fxgc6", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/4/6/dataset_f46e1805-e9f8-4e9a-9ea1-cd196d038e0a.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --samples-file \"/galaxy/server/database/objects/4/4/1/dataset_4415ae9d-9e1b-452a-86fe-f4d0b0b052b9.dat\" --ploidy-file '/galaxy/server/database/objects/d/2/1/dataset_d21bfe2a-02e8-4109-8e00-a59007c7bf33.dat' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/2/a/6/dataset_2a6e6c11-cec3-4b08-900f-745d1d0f79f9.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": false, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": null, \"skip_variants\": null, \"variants_only\": false}", "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": {\"values\": [{\"id\": 91, \"src\": \"hda\"}]}, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 0, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}, \"gvcf\": \"\", \"method\": \"multiallelic\", \"prior\": \"0.0011\", \"prior_freqs\": \"\"}}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": {\"values\": [{\"id\": 90, \"src\": \"hda\"}]}}"}, "inputs": {"input_file": {"id": "e5e85752534a1f6b", "src": "hda", "uuid": "f46e1805-e9f8-4e9a-9ea1-cd196d038e0a"}, "sec_restrict|samples_file": {"id": "c9147cfbb24d024f", "src": "hda", "uuid": "4415ae9d-9e1b-452a-86fe-f4d0b0b052b9"}, "sec_file_format|ploidy_file": {"id": "d58abde2fb36f1e8", "src": "hda", "uuid": "d21bfe2a-02e8-4109-8e00-a59007c7bf33"}}, "outputs": {"output_file": {"id": "748366871c7f2141", "src": "hda", "uuid": "2a6e6c11-cec3-4b08-900f-745d1d0f79f9"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-14 01:04:14", "plugin": "core", "name": "end_epoch", "raw_value": "1726275854.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:04:13", "plugin": "core", "name": "start_epoch", "raw_value": "1726275853.0000000"}, {"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_call/1.15.1+galaxy5-3", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 3, "time_seconds": 27.42010807991028, "inputs": {"input_file": {"src": "hda", "id": "fb8ab536889f0e94"}, "sec_consensus_variant_calling|variant_calling|method": "consensus", "sec_file_format|ploidy_file": {"src": "hda", "id": "153dc00d25d9a6d7"}, "output_type": "v"}, "job": {"model_class": "Job", "id": "b94e2d0d46c75809", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:04:51.055051", "create_time": "2024-09-14T01:04:41.441874", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "history_id": "ed165837e8ba4cca", "external_id": "gxy-648pz", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/0/1/6/dataset_0169bfe6-0746-4748-9eb6-acd70fc7c9b7.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -c --pval-threshold 0.5 --ploidy-file '/galaxy/server/database/objects/1/7/a/dataset_17a8daa3-95a4-40f0-b5c9-34b72456c79d.dat' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/3/3/5/dataset_3354dc69-b987-4dde-a2c6-85b31ef2c0fc.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": false, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": null, \"skip_variants\": null, \"variants_only\": false}", "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": {\"values\": [{\"id\": 94, \"src\": \"hda\"}]}, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 1, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\"}, \"method\": \"consensus\", \"pval_threshold\": \"0.5\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}"}, "inputs": {"input_file": {"id": "fb8ab536889f0e94", "src": "hda", "uuid": "0169bfe6-0746-4748-9eb6-acd70fc7c9b7"}, "sec_file_format|ploidy_file": {"id": "153dc00d25d9a6d7", "src": "hda", "uuid": "17a8daa3-95a4-40f0-b5c9-34b72456c79d"}}, "outputs": {"output_file": {"id": "50976ab105970f33", "src": "hda", "uuid": "3354dc69-b987-4dde-a2c6-85b31ef2c0fc"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-14 01:04:44", "plugin": "core", "name": "end_epoch", "raw_value": "1726275884.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:04:43", "plugin": "core", "name": "start_epoch", "raw_value": "1726275883.0000000"}, {"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_call/1.15.1+galaxy5-4", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 4, "time_seconds": 27.633683919906616, "inputs": {"input_file": {"src": "hda", "id": "b914c5cbdc32f1b4"}, "sec_consensus_variant_calling|variant_calling|method": "consensus", "sec_file_format|ploidy_file": {"src": "hda", "id": "022a03c7fd9fc863"}, "sec_input_output|output_tags": "INFO/PV4", "output_type": "v"}, "job": {"model_class": "Job", "id": "0dd086a5fc3869bf", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:05:18.846615", "create_time": "2024-09-14T01:05:08.377633", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "history_id": "ed165837e8ba4cca", "external_id": "gxy-9ncpq", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/2/8/0/dataset_280c6e28-ddda-4b08-b70b-63b33c482628.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -c --pval-threshold 0.5 --ploidy-file '/galaxy/server/database/objects/e/8/c/dataset_e8ce517b-35d8-4f05-a500-27ed2a854b76.dat' --annotate INFO/PV4 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/a/5/1/dataset_a51cf330-c1c4-4b13-8f9d-c8e5ff207911.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": false, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": \"INFO/PV4\", \"skip_variants\": null, \"variants_only\": false}", "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": {\"values\": [{\"id\": 97, \"src\": \"hda\"}]}, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 1, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\"}, \"method\": \"consensus\", \"pval_threshold\": \"0.5\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}"}, "inputs": {"input_file": {"id": "b914c5cbdc32f1b4", "src": "hda", "uuid": "280c6e28-ddda-4b08-b70b-63b33c482628"}, "sec_file_format|ploidy_file": {"id": "022a03c7fd9fc863", "src": "hda", "uuid": "e8ce517b-35d8-4f05-a500-27ed2a854b76"}}, "outputs": {"output_file": {"id": "9286c7c1ce47fbe4", "src": "hda", "uuid": "a51cf330-c1c4-4b13-8f9d-c8e5ff207911"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-14 01:05:10", "plugin": "core", "name": "end_epoch", "raw_value": "1726275910.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:05:09", "plugin": "core", "name": "start_epoch", "raw_value": "1726275909.0000000"}, {"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_call/1.15.1+galaxy5-5", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 5, "time_seconds": 27.147149085998535, "inputs": {"input_file": {"src": "hda", "id": "34c46068446c92bb"}, "sec_restrict|regions_overlap": "1", "sec_consensus_variant_calling|variant_calling|method": "multiallelic", "sec_input_output|variants_only": true, "output_type": "v"}, "job": {"model_class": "Job", "id": "050fdb9488518af8", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:05:46.323294", "create_time": "2024-09-14T01:05:35.858303", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "history_id": "ed165837e8ba4cca", "external_id": "gxy-gqh4b", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/c/c/b/dataset_ccb9add7-6130-4226-b9ff-91874809a4d9.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --regions-overlap 1 --variants-only --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/9/f/4/dataset_9f43a52e-df3f-4799-bda3-48f718656361.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": false, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": null, \"skip_variants\": null, \"variants_only\": true}", "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 0, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}, \"gvcf\": \"\", \"method\": \"multiallelic\", \"prior\": \"0.0011\", \"prior_freqs\": \"\"}}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": \"1\", \"samples\": \"\", \"samples_file\": null}"}, "inputs": {"input_file": {"id": "34c46068446c92bb", "src": "hda", "uuid": "ccb9add7-6130-4226-b9ff-91874809a4d9"}}, "outputs": {"output_file": {"id": "45622d042ca95d2d", "src": "hda", "uuid": "9f43a52e-df3f-4799-bda3-48f718656361"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n", "job_stdout": "", "job_stderr": "", "stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-14 01:05:38", "plugin": "core", "name": "end_epoch", "raw_value": "1726275938.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:05:37", "plugin": "core", "name": "start_epoch", "raw_value": "1726275937.0000000"}, {"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_call/1.15.1+galaxy5-6", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 6, "time_seconds": 27.390697240829468, "inputs": {"input_file": {"src": "hda", "id": "4807d53d9a2e2e7f"}, "sec_consensus_variant_calling|variant_calling|method": "multiallelic", "sec_input_output|group_samples": true, "output_type": "v"}, "job": {"model_class": "Job", "id": "16a1aab48891616f", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:06:13.822806", "create_time": "2024-09-14T01:06:03.263203", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "history_id": "ed165837e8ba4cca", "external_id": "gxy-xgwps", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/5/c/7/dataset_5c73108f-7db9-4e2e-9762-31df7ea70502.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --group-samples - --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/f/7/4/dataset_f7421e87-a418-4b27-9fa0-562c91b117c2.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": true, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": null, \"skip_variants\": null, \"variants_only\": false}", "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 0, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}, \"gvcf\": \"\", \"method\": \"multiallelic\", \"prior\": \"0.0011\", \"prior_freqs\": \"\"}}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}"}, "inputs": {"input_file": {"id": "4807d53d9a2e2e7f", "src": "hda", "uuid": "5c73108f-7db9-4e2e-9762-31df7ea70502"}}, "outputs": {"output_file": {"id": "cc384397a197f1fe", "src": "hda", "uuid": "f7421e87-a418-4b27-9fa0-562c91b117c2"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n", "job_stdout": "", "job_stderr": "", "stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-14 01:06:05", "plugin": "core", "name": "end_epoch", "raw_value": "1726275965.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:06:05", "plugin": "core", "name": "start_epoch", "raw_value": "1726275965.0000000"}, {"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_call/1.15.1+galaxy5-7", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 7, "time_seconds": 22.75749182701111, "inputs": {"input_file": {"src": "hda", "id": "4f3352db0d5bc390"}, "sec_consensus_variant_calling|variant_calling|genotypes|targets|targets_file": {"src": "hda", "id": "cbd23c4cd10aa88a"}, "sec_consensus_variant_calling|variant_calling|genotypes|targets|targets_src": "targets_file", "sec_consensus_variant_calling|variant_calling|method": "multiallelic", "output_type": "v"}, "job": {"model_class": "Job", "id": "f513f03dee6ba111", "state": "error", "exit_code": null, "update_time": "2024-09-14T01:06:36.828805", "create_time": "2024-09-14T01:06:31.054100", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "history_id": "ed165837e8ba4cca", "external_id": "gxy-tbxfz", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/b/8/5/dataset_b851b4ac-86be-4622-bbe1-cc1c4d60f388.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --targets-file \"/galaxy/server/database/objects/f/9/a/dataset_f9ab92a9-992d-4798-8921-d967a0352f8b.dat\" --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/a/1/a/dataset_a1aa4eef-f0a9-4302-bc82-9e4cd2d6448a.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": false, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": null, \"skip_variants\": null, \"variants_only\": false}", "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 0, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\", \"targets\": {\"__current_case__\": 2, \"invert_targets_file\": false, \"targets_file\": {\"values\": [{\"id\": 104, \"src\": \"hda\"}]}, \"targets_src\": \"targets_file\"}, \"targets_overlap\": null}, \"gvcf\": \"\", \"method\": \"multiallelic\", \"prior\": \"0.0011\", \"prior_freqs\": \"\"}}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}"}, "inputs": {"input_file": {"id": "4f3352db0d5bc390", "src": "hda", "uuid": "b851b4ac-86be-4622-bbe1-cc1c4d60f388"}, "sec_consensus_variant_calling|variant_calling|genotypes|targets|targets_file": {"id": "cbd23c4cd10aa88a", "src": "hda", "uuid": "f9ab92a9-992d-4798-8921-d967a0352f8b"}}, "outputs": {"output_file": {"id": "fb28fb836c18096d", "src": "hda", "uuid": "a1aa4eef-f0a9-4302-bc82-9e4cd2d6448a"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stderr": "", "stdout": "", "job_messages": null, "dependencies": [], "user_email": "tests@fake.org", "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "bcftools_plugin_setgt/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_plugin_setgt", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 29.494212865829468, "inputs": {"input_file": {"src": "hda", "id": "050fdb9488518af8"}, "sec_plugin|target_gt": ".", "sec_plugin|new_gt": "0", "output_type": "v"}, "job": {"model_class": "Job", "id": "5138b028115a7f5f", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:02:43.260801", "create_time": "2024-09-14T01:02:28.376183", "galaxy_version": "23.1", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4", "history_id": "ed165837e8ba4cca", "external_id": "gxy-sj7c8", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/0/e/c/dataset_0ec80de0-a6fe-4a06-8f08-57c3644d56d6.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin setGT --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz -- --target-gt '.' --new-gt '0' > '/galaxy/server/database/objects/6/4/c/dataset_64c559e1-7737-44d9-975a-b916868431a1.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_plugin": "{\"new_gt\": \"0\", \"target_gt\": \".\"}", "sec_restrict": "{\"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "050fdb9488518af8", "src": "hda", "uuid": "0ec80de0-a6fe-4a06-8f08-57c3644d56d6"}}, "outputs": {"output_file": {"id": "1913c0b28f54e065", "src": "hda", "uuid": "64c559e1-7737-44d9-975a-b916868431a1"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Filled 44 alleles\n", "job_stdout": "", "job_stderr": "", "stderr": "Filled 44 alleles\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 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Doing first pass of vcf\nMTC application completed\nSuccessful exit.\n", "job_stdout": "", "job_stderr": "", "stderr": "Skipping default settings\nAt least one type of multiple testing correction requested. Doing first pass of vcf\nMTC application completed\nSuccessful exit.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-14 01:11:56", "plugin": "core", "name": "end_epoch", "raw_value": "1726276316.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:11:56", "plugin": "core", "name": "start_epoch", "raw_value": "1726276316.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "lofreq_filter/2.1.5+galaxy0-1", "has_data": true, "data": {"tool_id": "lofreq_filter", "tool_version": "2.1.5+galaxy0", "test_index": 1, "time_seconds": 26.44701385498047, "inputs": {"invcf": {"src": "hda", "id": "2cd1d76bf2ef465f"}, "filter_by_type|qual|snvqual_filter|snvqual_alpha": "0.01", "filter_by_type|qual|snvqual_filter|snvqual_mtc": "bonf", "filter_by_type|qual|snvqual_filter|snvqual_ntests": "66", "filter_by_type|qual|snvqual_filter|snvqual": "mtc", "filter_by_type|keep_only": "--only-snvs"}, "job": {"model_class": "Job", "id": "ffe3188988274058", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:12:32.874760", "create_time": "2024-09-14T01:12:23.158742", "galaxy_version": "23.1", "command_version": "2.1.5", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0", "history_id": "ed165837e8ba4cca", "external_id": "gxy-z7zd4", "command_line": "lofreq filter -i /galaxy/server/database/objects/b/b/7/dataset_bb79af39-540f-476a-8499-ce98d1bb4930.dat --no-defaults --verbose --only-snvs -q bonf -r 0.01 -s 66 -v 10 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001 -o filtered.vcf", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "flag_or_drop": "\"\"", "sb": "{\"sb_filter\": {\"__current_case__\": 2, \"sb_alpha\": \"0.001\", \"sb_compound\": true, \"sb_indels\": false, \"sb_mtc\": \"fdr\", \"strand_bias\": \"mtc\"}}", "af": "{\"af_max\": \"0.0\", \"af_min\": \"0.0\"}", "coverage": "{\"cov_max\": \"0\", \"cov_min\": \"10\"}", "filter_by_type": "{\"__current_case__\": 1, \"keep_only\": \"--only-snvs\", \"qual\": {\"snvqual_filter\": {\"__current_case__\": 2, \"snvqual\": \"mtc\", \"snvqual_alpha\": \"0.01\", \"snvqual_mtc\": \"bonf\", \"snvqual_ntests\": \"66\"}}}"}, "inputs": {"invcf": {"id": "2cd1d76bf2ef465f", "src": "hda", "uuid": "bb79af39-540f-476a-8499-ce98d1bb4930"}}, "outputs": {"outvcf": {"id": "b7c0a16325039497", "src": "hda", "uuid": "fc537fb9-1af0-4abb-ac6b-c6d2c675d2f8"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Skipping default settings\nAt least one type of multiple testing correction requested. Doing first pass of vcf\nMTC application completed\nSuccessful exit.\n", "job_stdout": "", "job_stderr": "", "stderr": "Skipping default settings\nAt least one type of multiple testing correction requested. Doing first pass of vcf\nMTC application completed\nSuccessful exit.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-14 01:12:24", "plugin": "core", "name": "end_epoch", "raw_value": "1726276344.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:12:24", "plugin": "core", "name": "start_epoch", "raw_value": "1726276344.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "lofreq_filter/2.1.5+galaxy0-2", "has_data": true, "data": {"tool_id": "lofreq_filter", "tool_version": "2.1.5+galaxy0", "test_index": 2, "time_seconds": 25.733057498931885, "inputs": {"invcf": {"src": "hda", "id": "8e44a153c95d11b1"}, "filter_by_type|qual|snvqual_filter|snvqual_thresh": "38", "filter_by_type|qual|snvqual_filter|snvqual": "min-phred", "filter_by_type|qual|indelqual_filter|indelqual_thresh": "20", "filter_by_type|qual|indelqual_filter|indelqual": "min-phred", "flag_or_drop": "--print-all"}, "job": {"model_class": "Job", "id": "22470166765b2f95", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:12:59.097096", "create_time": "2024-09-14T01:12:48.376072", "galaxy_version": "23.1", "command_version": "2.1.5", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0", "history_id": "ed165837e8ba4cca", "external_id": "gxy-vjsz6", "command_line": "lofreq filter -i /galaxy/server/database/objects/2/b/9/dataset_2b9714b6-244b-4f44-99c5-d96ed5ed26bb.dat --no-defaults --verbose --print-all -Q 38 -K 20 -v 10 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001 -o filtered.vcf", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "flag_or_drop": "\"--print-all\"", "sb": "{\"sb_filter\": {\"__current_case__\": 2, \"sb_alpha\": \"0.001\", \"sb_compound\": true, \"sb_indels\": false, \"sb_mtc\": \"fdr\", \"strand_bias\": \"mtc\"}}", "af": "{\"af_max\": \"0.0\", \"af_min\": \"0.0\"}", "coverage": "{\"cov_max\": \"0\", \"cov_min\": \"10\"}", "filter_by_type": "{\"__current_case__\": 0, \"keep_only\": \"\", \"qual\": {\"indelqual_filter\": {\"__current_case__\": 1, \"indelqual\": \"min-phred\", \"indelqual_thresh\": \"20\"}, \"snvqual_filter\": {\"__current_case__\": 1, \"snvqual\": \"min-phred\", \"snvqual_thresh\": \"38\"}}}"}, "inputs": {"invcf": {"id": "8e44a153c95d11b1", "src": "hda", "uuid": "2b9714b6-244b-4f44-99c5-d96ed5ed26bb"}}, "outputs": {"outvcf": {"id": "cdedced2495e5cfa", "src": "hda", "uuid": "fa906c50-95ff-404f-8ac9-e2034872902d"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Skipping default settings\nAt least one type of multiple testing correction requested. Doing first pass of vcf\nMTC application completed\nSuccessful exit.\n", "job_stdout": "", "job_stderr": "", "stderr": "Skipping default settings\nAt least one type of multiple testing correction requested. Doing first pass of vcf\nMTC application completed\nSuccessful exit.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-14 01:12:50", "plugin": "core", "name": "end_epoch", "raw_value": "1726276370.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:12:49", "plugin": "core", "name": "start_epoch", "raw_value": "1726276369.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "mummer_mummerplot/4.0.0rc1+galaxy3-0", "has_data": true, "data": {"tool_id": "mummer_mummerplot", "tool_version": "4.0.0rc1+galaxy3", "test_index": 0, "time_seconds": 56.06736159324646, "inputs": {"delta": {"src": "hda", "id": "5b9dd8b4f1931ef0"}, "reference_sequence": {"src": "hda", "id": "c88e0a7c4b227092"}, "query_sequence": {"src": "hda", "id": "3af2ba6b49342b39"}, "sequences|seq_input": "no", "extra_outs": "all"}, "job": {"model_class": "Job", "id": "b7c0a16325039497", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:16:59.690383", "create_time": "2024-09-14T01:16:27.384761", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0rc1+galaxy3", "history_id": "ed165837e8ba4cca", "external_id": "gxy-pq6wf", "command_line": "ln -s /galaxy/server/database/objects/6/e/1/dataset_6e10fecc-c97b-4ca7-9da4-c40cc1d42723.dat reference.fa && ln -s /galaxy/server/database/objects/4/a/4/dataset_4a48162c-a92c-4aa7-9e4c-28aae13d71e1.dat query.fa && mummerplot -b '20' -s 'small' -terminal png -title 'Title' '/galaxy/server/database/objects/7/5/0/dataset_75030957-c55c-4285-b8e0-e34c7fe01ce7.dat' && gnuplot < out.gp", "traceback": null, "params": {"__input_ext": "\"input\"", "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": "5b9dd8b4f1931ef0", "src": "hda", "uuid": "75030957-c55c-4285-b8e0-e34c7fe01ce7"}, "reference_sequence": {"id": "c88e0a7c4b227092", "src": "hda", "uuid": "6e10fecc-c97b-4ca7-9da4-c40cc1d42723"}, "query_sequence": {"id": "3af2ba6b49342b39", "src": "hda", "uuid": "4a48162c-a92c-4aa7-9e4c-28aae13d71e1"}}, "outputs": {"gnuplot": {"id": "e6b561534f113681", "src": "hda", "uuid": "94263f6d-1ddc-405a-9095-6acd338bb982"}, "fplot": {"id": "d0aab521f6ac753c", "src": "hda", "uuid": "d0734c92-fe76-4825-92ed-ed4843743318"}, "rplot": {"id": "fc7b988d9d93f613", "src": "hda", "uuid": "6199b110-e8f3-4255-b15e-2a18875c43dc"}, "hplot": {"id": "3e19916a2d2e7ee6", "src": "hda", "uuid": "0816ce20-2b69-4ed0-acd4-29c3a99e3349"}, "output_png": {"id": "d499619175dc1fe3", "src": "hda", "uuid": "36c0cffd-d993-4c16-8e58-f62a3e6731b2"}}, "output_collections": {}, "tool_stdout": "gnuplot 5.4 patchlevel 8\n", "tool_stderr": "WARNING: Could not open /tmp/tmpk0v09mol/files/2/f/7/dataset_2f771d7a-b9f1-4fc9-b1ea-d06b84d013a0.dat, No such file or directory\nWARNING: Trouble closing /tmp/tmpk0v09mol/files/2/f/7/dataset_2f771d7a-b9f1-4fc9-b1ea-d06b84d013a0.dat, Bad file descriptor\nWARNING: Could not open /tmp/tmpk0v09mol/files/d/1/b/dataset_d1bcd825-fbc8-415a-9896-a6af5fd5ebaa.dat, No such file or directory\nWARNING: Trouble closing /tmp/tmpk0v09mol/files/d/1/b/dataset_d1bcd825-fbc8-415a-9896-a6af5fd5ebaa.dat, Bad file descriptor\nReading delta file /galaxy/server/database/objects/7/5/0/dataset_75030957-c55c-4285-b8e0-e34c7fe01ce7.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": "", "stderr": "WARNING: Could not open /tmp/tmpk0v09mol/files/2/f/7/dataset_2f771d7a-b9f1-4fc9-b1ea-d06b84d013a0.dat, No such file or directory\nWARNING: Trouble closing /tmp/tmpk0v09mol/files/2/f/7/dataset_2f771d7a-b9f1-4fc9-b1ea-d06b84d013a0.dat, Bad file descriptor\nWARNING: Could not open /tmp/tmpk0v09mol/files/d/1/b/dataset_d1bcd825-fbc8-415a-9896-a6af5fd5ebaa.dat, No such file or directory\nWARNING: Trouble closing /tmp/tmpk0v09mol/files/d/1/b/dataset_d1bcd825-fbc8-415a-9896-a6af5fd5ebaa.dat, Bad file descriptor\nReading delta file /galaxy/server/database/objects/7/5/0/dataset_75030957-c55c-4285-b8e0-e34c7fe01ce7.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", "stdout": "gnuplot 5.4 patchlevel 8\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-14 01:16:43", "plugin": "core", "name": "end_epoch", "raw_value": "1726276603.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:16:43", "plugin": "core", "name": "start_epoch", "raw_value": "1726276603.0000000"}, {"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_occupancy/0.6.1a1.1-0", "has_data": true, "data": {"tool_id": "poretools_occupancy", "tool_version": "0.6.1a1.1", "test_index": 0, "time_seconds": 52.44715332984924, "inputs": {"input": {"src": "hda", "id": "a5bab748014374bb"}, "extension": "png", "plot_type": "read_count"}, "job": {"model_class": "Job", "id": "50976ab105970f33", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:08:56.406003", "create_time": "2024-09-14T01:08:20.819103", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-ntslm", "command_line": "export MPLBACKEND=\"agg\" && poretools occupancy '/galaxy/server/database/objects/6/2/b/dataset_62b11c17-ec6c-4bc4-8a13-8e3dc741307e.dat' --saveas occupancy.png --plot-type read_count && mv occupancy.png '/galaxy/server/database/objects/4/b/3/dataset_4b3c64f9-a60d-461a-9d32-070e41cada4e.dat'", "traceback": null, "params": {"__input_ext": "\"fast5.tar\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "plot_type": "\"read_count\"", "extension": "\"png\""}, "inputs": {"input": {"id": "a5bab748014374bb", "src": "hda", "uuid": "62b11c17-ec6c-4bc4-8a13-8e3dc741307e"}}, "outputs": {"output": {"id": "bd5e06df4cb7f9fc", "src": "hda", "uuid": "4b3c64f9-a60d-461a-9d32-070e41cada4e"}}, "output_collections": {}, "tool_stdout": "channel_number\tstart_time\tduration\n128\t1457127626\t1\n128\t1457129549\t4\n126\t1457148908\t5\n126\t1457129771\t6\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "channel_number\tstart_time\tduration\n128\t1457127626\t1\n128\t1457129549\t4\n126\t1457148908\t5\n126\t1457129771\t6\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-09-14 01:08:39", "plugin": "core", "name": "end_epoch", "raw_value": "1726276119.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:08:36", "plugin": "core", "name": "start_epoch", "raw_value": "1726276116.0000000"}, {"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_occupancy/0.6.1a1.1-1", "has_data": true, "data": {"tool_id": "poretools_occupancy", "tool_version": "0.6.1a1.1", "test_index": 1, "time_seconds": 28.9235782623291, "inputs": {"input": {"src": "hda", "id": "03016dc1802ebe2b"}, "extension": "pdf", "plot_type": "total_bp"}, "job": {"model_class": "Job", "id": "022a03c7fd9fc863", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:09:25.677885", "create_time": "2024-09-14T01:09:12.956134", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-shnr9", "command_line": "export MPLBACKEND=\"agg\" && poretools occupancy '/galaxy/server/database/objects/a/3/d/dataset_a3d686e3-815f-4a4b-8be3-f9a3dce3945e.dat' --saveas occupancy.pdf --plot-type total_bp && mv occupancy.pdf '/galaxy/server/database/objects/1/c/a/dataset_1ca7c8ab-b06c-4fce-9238-a1f3e4e61b28.dat'", "traceback": null, "params": {"__input_ext": "\"fast5.tar\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "plot_type": "\"total_bp\"", "extension": "\"pdf\""}, "inputs": {"input": {"id": "03016dc1802ebe2b", "src": "hda", "uuid": "a3d686e3-815f-4a4b-8be3-f9a3dce3945e"}}, "outputs": {"output": {"id": "38d82a18eaba87f9", "src": "hda", "uuid": "1ca7c8ab-b06c-4fce-9238-a1f3e4e61b28"}}, "output_collections": {}, "tool_stdout": "channel_number\tstart_time\tduration\n128\t1457127626\t1\n128\t1457129549\t4\n126\t1457148908\t5\n126\t1457129771\t6\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "channel_number\tstart_time\tduration\n128\t1457127626\t1\n128\t1457129549\t4\n126\t1457148908\t5\n126\t1457129771\t6\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-09-14 01:09:17", "plugin": "core", "name": "end_epoch", "raw_value": "1726276157.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:09:14", "plugin": "core", "name": "start_epoch", "raw_value": "1726276154.0000000"}, {"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": "salmon/1.3.0+galaxy1-0", "has_data": true, "data": {"tool_id": "salmon", "tool_version": "1.3.0+galaxy1", "test_index": 0, "time_seconds": 43.32157373428345, "inputs": {"quant_type|refTranscriptSource|s_index|fasta": {"src": "hda", "id": "e190026cff40e92e"}, "quant_type|refTranscriptSource|TranscriptSource": "history", "quant_type|writeMappings": true, "quant_type|qtype": "reads"}, "job": {"model_class": "Job", "id": "bd5e06df4cb7f9fc", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:13:43.159739", "create_time": "2024-09-14T01:13:15.618510", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-rft4f", "command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/3/d/a/dataset_3da24e97-7ec8-4b05-8355-23ca0794c723.dat' && ln -s /galaxy/server/database/objects/3/d/a/dataset_3da24e97-7ec8-4b05-8355-23ca0794c723.dat ./single.fasta && salmon quant --index './index' --libType U --unmatedReads ./single.fasta --threads \"${GALAXY_SLOTS:-4}\" --writeMappings=./output/samout.sam --incompatPrior '0.0' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '100' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '1e-05' -o ./output && samtools sort -@ ${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam ./output/samout.sam", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"biasSpeedSamp\": \"5\", \"bootstrapReproject\": false, \"dumpEq\": false, \"dumpEqWeights\": false, \"fldMax\": \"1000\", \"fldMean\": \"250\", \"fldSD\": \"25\", \"forgettingFactor\": \"0.65\", \"initUniform\": false, \"maxReadOcc\": \"100\", \"minAssignedFrags\": \"\", \"noBiasLengthThreshold\": false, \"noEffectiveLengthCorrection\": false, \"noFragLengthDist\": false, \"noGammaDraw\": false, \"noLengthCorrection\": false, \"numAuxModelSamples\": \"5000000\", \"numBiasSamples\": \"2000000\", \"numBootstraps\": \"0\", \"numGibbsSamples\": \"0\", \"numPreAuxModelSamples\": \"5000\", \"perTranscriptPrior\": false, \"rangeFactorizationBins\": \"0\", \"sigDigits\": \"3\", \"skipQuant\": false, \"thinningFactor\": \"16\", \"useEM\": false, \"vbPrior\": \"1e-05\", \"writeOrphanLinks\": false, \"writeUnmappedNames\": false}", "meta": "false", "incompatPrior": "\"0.0\"", "gcBias": "false", "seqBias": "false", "geneMap": null, "quant_type": "{\"__current_case__\": 0, \"consensusSlack\": \"0\", \"consistentHits\": false, \"discardOrphansQuasi\": false, \"dovetail\": false, \"input\": {\"single_or_paired\": {\"__current_case__\": 0, \"input_singles\": {\"values\": [{\"id\": 131, \"src\": \"hda\"}]}, \"single_or_paired_opts\": \"single\", \"strandedness\": \"U\"}}, \"qtype\": \"reads\", \"quasiCoverage\": \"\", \"recoverOrphans\": false, \"refTranscriptSource\": {\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 131, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}, \"type\": \"quasi\", \"validmap\": {\"__current_case__\": 1, \"validateMappings\": false}, \"writeMappings\": true}"}, "inputs": {"quant_type|refTranscriptSource|s_index|fasta": {"id": "e190026cff40e92e", "src": "hda", "uuid": "3da24e97-7ec8-4b05-8355-23ca0794c723"}, "quant_type|input|single_or_paired|input_singles": {"id": "e190026cff40e92e", "src": "hda", "uuid": "3da24e97-7ec8-4b05-8355-23ca0794c723"}}, "outputs": {"output_quant": {"id": "7129595db7e043e5", "src": "hda", "uuid": "44357ab7-cf8e-49dc-9ead-fe2492d3662c"}, "output_bam": {"id": "5e5c3dd04dd5085d", "src": "hda", "uuid": "a2b4fd54-4e08-4407-bf50-d29c5625abc9"}}, "output_collections": {}, "tool_stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 14\nFalse junctions count = 17\nHash table size = 31\nCandidate marks count = 54\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 51\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 14\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 105024 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "tool_stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n[2024-09-14 01:13:29.468] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-09-14 01:13:29.468] [jLog] [info] building index\nout : ./index\n[2024-09-14 01:13:29.469] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-09-14 01:13:29.477] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-09-14 01:13:29.477] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 15 cleaned references\n[2024-09-14 01:13:29.490] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-09-14 01:13:29.492] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20\nallowedIn: 12\nMax Junction ID: 70\nseen.size():569 kmerInfo.size():71\napproximateContigTotalLength: 17465\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 24 element count: 19592 complex nodes: 0\n# of ones in rank vector: 23\n[2024-09-14 01:13:29.550] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-09-14 01:13:29.550] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 19592\n-----------------------------------------\n| Loading contigs | Time = 1.3544 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading contig boundaries | Time = 858.55 us\n-----------------------------------------\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n23\n[2024-09-14 01:13:29.552] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-09-14 01:13:29.552] [puff::index::jointLog] [info] contig count for validation: 23\n[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] Total # of Contigs : 23\n[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] Total # of numerical Contigs : 23\n[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] Total # of contig vec entries: 36\n[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] bits per offset entry 6\n[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] Done constructing the contig vector. 24\n[2024-09-14 01:13:29.564] [puff::index::jointLog] [info] # segments = 23\n[2024-09-14 01:13:29.564] [puff::index::jointLog] [info] total length = 19592\n[2024-09-14 01:13:29.564] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] positional integer width = 15\n[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] seqSize = 19592\n[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] rankSize = 19592\n[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] num keys = 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min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-09-14 01:13:29.659] [puff::index::jointLog] [info] mphf size = 0.0125198 MB\n[2024-09-14 01:13:29.659] [puff::index::jointLog] [info] chunk size = 9796\n[2024-09-14 01:13:29.659] [puff::index::jointLog] [info] chunk 0 = [0, 9796)\n[2024-09-14 01:13:29.659] [puff::index::jointLog] [info] chunk 1 = [9796, 19562)\n[2024-09-14 01:13:29.660] [puff::index::jointLog] [info] finished populating pos vector\n[2024-09-14 01:13:29.660] [puff::index::jointLog] [info] writing index components\n[2024-09-14 01:13:29.674] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-09-14 01:13:29.681] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n### salmon (selective-alignment-based) v1.3.0\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { U }\n### [ unmatedReads ] => { ./single.fasta }\n### [ threads ] => { 6 }\n### [ writeMappings ] => { ./output/samout.sam }\n### [ incompatPrior ] => { 0.0 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 100 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 1e-05 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n[2024-09-14 01:13:30.154] [jointLog] [info] setting maxHashResizeThreads to 6\n[2024-09-14 01:13:30.154] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-09-14 01:13:30.154] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-09-14 01:13:30.154] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.\n[2024-09-14 01:13:30.154] [jointLog] [info] parsing read library format\n[2024-09-14 01:13:30.154] [jointLog] [info] There is 1 library.\n-----------------------------------------\n| Loading contig table | Time = 965.86 us\n-----------------------------------------\nsize = 24\n-----------------------------------------\n| Loading contig offsets | Time = 1.6044 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 715.63 us\n-----------------------------------------\n[2024-09-14 01:13:30.248] [jointLog] [info] Loading pufferfish index\n[2024-09-14 01:13:30.249] [jointLog] [info] Loading dense pufferfish index.\n-----------------------------------------\n| Loading mphf table | Time = 802.15 us\n-----------------------------------------\nsize = 19592\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 1.1211 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading sequence | Time = 792.46 us\n-----------------------------------------\nsize = 18902\n-----------------------------------------\n| Loading positions | Time = 1.5093 ms\n-----------------------------------------\nsize = 28562\n-----------------------------------------\n| Loading reference sequence | Time = 737.14 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 430.98 us\n-----------------------------------------\n[2024-09-14 01:13:30.260] [jointLog] [info] done\n[2024-09-14 01:13:30.260] [jointLog] [info] Index contained 15 targets\n[2024-09-14 01:13:30.260] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2024-09-14 01:13:30.307] [jointLog] [info] Computed 15 rich equivalence classes for further processing\n[2024-09-14 01:13:30.307] [jointLog] [info] Counted 15 total reads in the equivalence classes \n[2024-09-14 01:13:30.308] [jointLog] [info] Number of mappings discarded because of alignment score : 5\n[2024-09-14 01:13:30.308] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2024-09-14 01:13:30.308] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-09-14 01:13:30.308] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2024-09-14 01:13:30.308] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2024-09-14 01:13:30.308] [jointLog] [info] Mapping rate = 100%\n\n[2024-09-14 01:13:30.308] [jointLog] [info] finished quantifyLibrary()\n[2024-09-14 01:13:30.313] [jointLog] [info] Starting optimizer\n[2024-09-14 01:13:30.313] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2024-09-14 01:13:30.313] [jointLog] [info] iteration = 0 | max rel diff. = 0\n[2024-09-14 01:13:30.314] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2024-09-14 01:13:30.315] [jointLog] [info] Finished optimizer\n[2024-09-14 01:13:30.315] [jointLog] [info] writing output \n\n[2024-09-14 01:13:30.319] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "job_stdout": "", "job_stderr": "", "stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n[2024-09-14 01:13:29.468] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-09-14 01:13:29.468] [jLog] [info] building index\nout : ./index\n[2024-09-14 01:13:29.469] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-09-14 01:13:29.477] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-09-14 01:13:29.477] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 15 cleaned references\n[2024-09-14 01:13:29.490] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-09-14 01:13:29.492] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20\nallowedIn: 12\nMax Junction ID: 70\nseen.size():569 kmerInfo.size():71\napproximateContigTotalLength: 17465\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 24 element count: 19592 complex nodes: 0\n# of ones in rank vector: 23\n[2024-09-14 01:13:29.550] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-09-14 01:13:29.550] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 19592\n-----------------------------------------\n| Loading contigs | Time = 1.3544 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading contig boundaries | Time = 858.55 us\n-----------------------------------------\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n23\n[2024-09-14 01:13:29.552] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-09-14 01:13:29.552] [puff::index::jointLog] [info] contig count for validation: 23\n[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] Total # of Contigs : 23\n[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] Total # of numerical Contigs : 23\n[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] Total # of contig vec entries: 36\n[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] bits per offset entry 6\n[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] Done constructing the contig vector. 24\n[2024-09-14 01:13:29.564] [puff::index::jointLog] [info] # segments = 23\n[2024-09-14 01:13:29.564] [puff::index::jointLog] [info] total length = 19592\n[2024-09-14 01:13:29.564] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] positional integer width = 15\n[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] seqSize = 19592\n[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] rankSize = 19592\n[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] num keys = 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min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-09-14 01:13:29.659] [puff::index::jointLog] [info] mphf size = 0.0125198 MB\n[2024-09-14 01:13:29.659] [puff::index::jointLog] [info] chunk size = 9796\n[2024-09-14 01:13:29.659] [puff::index::jointLog] [info] chunk 0 = [0, 9796)\n[2024-09-14 01:13:29.659] [puff::index::jointLog] [info] chunk 1 = [9796, 19562)\n[2024-09-14 01:13:29.660] [puff::index::jointLog] [info] finished populating pos vector\n[2024-09-14 01:13:29.660] [puff::index::jointLog] [info] writing index components\n[2024-09-14 01:13:29.674] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-09-14 01:13:29.681] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n### salmon (selective-alignment-based) v1.3.0\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { U }\n### [ unmatedReads ] => { ./single.fasta }\n### [ threads ] => { 6 }\n### [ writeMappings ] => { ./output/samout.sam }\n### [ incompatPrior ] => { 0.0 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 100 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 1e-05 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n[2024-09-14 01:13:30.154] [jointLog] [info] setting maxHashResizeThreads to 6\n[2024-09-14 01:13:30.154] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-09-14 01:13:30.154] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-09-14 01:13:30.154] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.\n[2024-09-14 01:13:30.154] [jointLog] [info] parsing read library format\n[2024-09-14 01:13:30.154] [jointLog] [info] There is 1 library.\n-----------------------------------------\n| Loading contig table | Time = 965.86 us\n-----------------------------------------\nsize = 24\n-----------------------------------------\n| Loading contig offsets | Time = 1.6044 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 715.63 us\n-----------------------------------------\n[2024-09-14 01:13:30.248] [jointLog] [info] Loading pufferfish index\n[2024-09-14 01:13:30.249] [jointLog] [info] Loading dense pufferfish index.\n-----------------------------------------\n| Loading mphf table | Time = 802.15 us\n-----------------------------------------\nsize = 19592\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 1.1211 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading sequence | Time = 792.46 us\n-----------------------------------------\nsize = 18902\n-----------------------------------------\n| Loading positions | Time = 1.5093 ms\n-----------------------------------------\nsize = 28562\n-----------------------------------------\n| Loading reference sequence | Time = 737.14 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 430.98 us\n-----------------------------------------\n[2024-09-14 01:13:30.260] [jointLog] [info] done\n[2024-09-14 01:13:30.260] [jointLog] [info] Index contained 15 targets\n[2024-09-14 01:13:30.260] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2024-09-14 01:13:30.307] [jointLog] [info] Computed 15 rich equivalence classes for further processing\n[2024-09-14 01:13:30.307] [jointLog] [info] Counted 15 total reads in the equivalence classes \n[2024-09-14 01:13:30.308] [jointLog] [info] Number of mappings discarded because of alignment score : 5\n[2024-09-14 01:13:30.308] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2024-09-14 01:13:30.308] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-09-14 01:13:30.308] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2024-09-14 01:13:30.308] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2024-09-14 01:13:30.308] [jointLog] [info] Mapping rate = 100%\n\n[2024-09-14 01:13:30.308] [jointLog] [info] finished quantifyLibrary()\n[2024-09-14 01:13:30.313] [jointLog] [info] Starting optimizer\n[2024-09-14 01:13:30.313] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2024-09-14 01:13:30.313] [jointLog] [info] iteration = 0 | max rel diff. = 0\n[2024-09-14 01:13:30.314] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2024-09-14 01:13:30.315] [jointLog] [info] Finished optimizer\n[2024-09-14 01:13:30.315] [jointLog] [info] writing output \n\n[2024-09-14 01:13:30.319] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 14\nFalse junctions count = 17\nHash table size = 31\nCandidate marks count = 54\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 51\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 14\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 105024 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-14 01:13:30", "plugin": "core", "name": "end_epoch", "raw_value": "1726276410.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:13:29", "plugin": "core", "name": "start_epoch", "raw_value": "1726276409.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}]}, "status": "success"}}, {"id": "salmon/1.3.0+galaxy1-1", "has_data": true, "data": {"tool_id": "salmon", "tool_version": "1.3.0+galaxy1", "test_index": 1, "time_seconds": 28.742324113845825, "inputs": {"quant_type|refTranscriptSource|s_index|fasta": {"src": "hda", "id": "e15e08e3a50188bb"}, "quant_type|refTranscriptSource|TranscriptSource": "history", "quant_type|qtype": "reads"}, "job": {"model_class": "Job", "id": "38d82a18eaba87f9", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:14:12.314272", "create_time": "2024-09-14T01:13:59.815388", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-lslxh", "command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/6/3/f/dataset_63f66a26-8968-4a36-8a38-81c06d448f0a.dat' && ln -s /galaxy/server/database/objects/6/3/f/dataset_63f66a26-8968-4a36-8a38-81c06d448f0a.dat ./single.fasta && salmon quant --index './index' --libType U --unmatedReads ./single.fasta --threads \"${GALAXY_SLOTS:-4}\" --incompatPrior '0.0' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '100' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '1e-05' -o ./output", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"biasSpeedSamp\": \"5\", \"bootstrapReproject\": false, \"dumpEq\": false, \"dumpEqWeights\": false, \"fldMax\": \"1000\", \"fldMean\": \"250\", \"fldSD\": \"25\", \"forgettingFactor\": \"0.65\", \"initUniform\": false, \"maxReadOcc\": \"100\", \"minAssignedFrags\": \"\", \"noBiasLengthThreshold\": false, \"noEffectiveLengthCorrection\": false, \"noFragLengthDist\": false, \"noGammaDraw\": false, \"noLengthCorrection\": false, \"numAuxModelSamples\": \"5000000\", \"numBiasSamples\": \"2000000\", \"numBootstraps\": \"0\", \"numGibbsSamples\": \"0\", \"numPreAuxModelSamples\": \"5000\", \"perTranscriptPrior\": false, \"rangeFactorizationBins\": \"0\", \"sigDigits\": \"3\", \"skipQuant\": false, \"thinningFactor\": \"16\", \"useEM\": false, \"vbPrior\": \"1e-05\", \"writeOrphanLinks\": false, \"writeUnmappedNames\": false}", "meta": "false", "incompatPrior": "\"0.0\"", "gcBias": "false", "seqBias": "false", "geneMap": null, "quant_type": "{\"__current_case__\": 0, \"consensusSlack\": \"0\", \"consistentHits\": false, \"discardOrphansQuasi\": false, \"dovetail\": false, \"input\": {\"single_or_paired\": {\"__current_case__\": 0, \"input_singles\": {\"values\": [{\"id\": 134, \"src\": \"hda\"}]}, \"single_or_paired_opts\": \"single\", \"strandedness\": \"U\"}}, \"qtype\": \"reads\", \"quasiCoverage\": \"\", \"recoverOrphans\": false, \"refTranscriptSource\": {\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 134, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}, \"type\": \"quasi\", \"validmap\": {\"__current_case__\": 1, \"validateMappings\": false}, \"writeMappings\": false}"}, "inputs": {"quant_type|refTranscriptSource|s_index|fasta": {"id": "e15e08e3a50188bb", "src": "hda", "uuid": "63f66a26-8968-4a36-8a38-81c06d448f0a"}, "quant_type|input|single_or_paired|input_singles": {"id": "e15e08e3a50188bb", "src": "hda", "uuid": "63f66a26-8968-4a36-8a38-81c06d448f0a"}}, "outputs": {"output_quant": {"id": "38f90275423cb8ff", "src": "hda", "uuid": "5f0e78b7-19ef-4886-a58c-1c22e07fdb79"}}, "output_collections": {}, "tool_stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 14\nFalse junctions count = 18\nHash table size = 32\nCandidate marks count = 55\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 51\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 14\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 105024 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "tool_stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n[2024-09-14 01:14:01.864] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-09-14 01:14:01.864] [jLog] [info] building index\nout : ./index\n[2024-09-14 01:14:01.866] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-09-14 01:14:01.874] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-09-14 01:14:01.874] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 15 cleaned references\n[2024-09-14 01:14:01.886] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-09-14 01:14:01.888] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20\nallowedIn: 12\nMax Junction ID: 70\nseen.size():569 kmerInfo.size():71\napproximateContigTotalLength: 17465\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 24 element count: 19592 complex nodes: 0\n# of ones in rank vector: 23\n[2024-09-14 01:14:01.952] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-09-14 01:14:01.952] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 19592\n-----------------------------------------\n| Loading contigs | Time = 1.8348 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading contig boundaries | Time = 1.0511 ms\n-----------------------------------------\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n23\n[2024-09-14 01:14:01.955] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-09-14 01:14:01.955] [puff::index::jointLog] [info] contig count for validation: 23\n[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] Total # of Contigs : 23\n[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] Total # of numerical Contigs : 23\n[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] Total # of contig vec entries: 36\n[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] bits per offset entry 6\n[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] Done constructing the contig vector. 24\n[2024-09-14 01:14:01.970] [puff::index::jointLog] [info] # segments = 23\n[2024-09-14 01:14:01.970] [puff::index::jointLog] [info] total length = 19592\n[2024-09-14 01:14:01.970] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] positional integer width = 15\n[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] seqSize = 19592\n[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] rankSize = 19592\n[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] num keys = 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elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-09-14 01:14:02.084] [puff::index::jointLog] [info] mphf size = 0.0125198 MB\n[2024-09-14 01:14:02.084] [puff::index::jointLog] [info] chunk size = 9796\n[2024-09-14 01:14:02.084] [puff::index::jointLog] [info] chunk 0 = [0, 9796)\n[2024-09-14 01:14:02.084] [puff::index::jointLog] [info] chunk 1 = [9796, 19562)\n[2024-09-14 01:14:02.085] [puff::index::jointLog] [info] finished populating pos vector\n[2024-09-14 01:14:02.085] [puff::index::jointLog] [info] writing index components\n[2024-09-14 01:14:02.100] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-09-14 01:14:02.107] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n### salmon (selective-alignment-based) v1.3.0\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { U }\n### [ unmatedReads ] => { ./single.fasta }\n### [ threads ] => { 6 }\n### [ incompatPrior ] => { 0.0 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 100 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 1e-05 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n[2024-09-14 01:14:02.202] [jointLog] [info] setting maxHashResizeThreads to 6\n[2024-09-14 01:14:02.202] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-09-14 01:14:02.202] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-09-14 01:14:02.202] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.\n[2024-09-14 01:14:02.202] [jointLog] [info] parsing read library format\n[2024-09-14 01:14:02.202] [jointLog] [info] There is 1 library.\n-----------------------------------------\n| Loading contig table | Time = 1.1905 ms\n-----------------------------------------\nsize = 24\n-----------------------------------------\n| Loading contig offsets | Time = 1.7182 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 564.82 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 1.2042 ms\n-----------------------------------------\nsize = 19592\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 1.1029 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading sequence | Time = 952.18 us\n-----------------------------------------\nsize = 18902\n-----------------------------------------\n| Loading positions | Time = 1.5979 ms\n-----------------------------------------\nsize = 28562\n-----------------------------------------\n| Loading reference sequence | Time = 803.94 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 595.88 us\n-----------------------------------------\n[2024-09-14 01:14:02.288] [jointLog] [info] Loading pufferfish index\n[2024-09-14 01:14:02.289] [jointLog] [info] Loading dense pufferfish index.\n[2024-09-14 01:14:02.301] [jointLog] [info] done\n[2024-09-14 01:14:02.301] [jointLog] [info] Index contained 15 targets\n[2024-09-14 01:14:02.301] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2024-09-14 01:14:02.348] [jointLog] [info] Computed 15 rich equivalence classes for further processing\n[2024-09-14 01:14:02.348] [jointLog] [info] Counted 15 total reads in the equivalence classes \n[2024-09-14 01:14:02.349] [jointLog] [info] Number of mappings discarded because of alignment score : 5\n[2024-09-14 01:14:02.349] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2024-09-14 01:14:02.349] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-09-14 01:14:02.349] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2024-09-14 01:14:02.350] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2024-09-14 01:14:02.350] [jointLog] [info] Mapping rate = 100%\n\n[2024-09-14 01:14:02.350] [jointLog] [info] finished quantifyLibrary()\n[2024-09-14 01:14:02.354] [jointLog] [info] Starting optimizer\n[2024-09-14 01:14:02.355] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2024-09-14 01:14:02.355] [jointLog] [info] iteration = 0 | max rel diff. = 0\n[2024-09-14 01:14:02.356] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2024-09-14 01:14:02.357] [jointLog] [info] Finished optimizer\n[2024-09-14 01:14:02.357] [jointLog] [info] writing output \n\n[2024-09-14 01:14:02.362] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "job_stdout": "", "job_stderr": "", "stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n[2024-09-14 01:14:01.864] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-09-14 01:14:01.864] [jLog] [info] building index\nout : ./index\n[2024-09-14 01:14:01.866] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-09-14 01:14:01.874] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-09-14 01:14:01.874] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 15 cleaned references\n[2024-09-14 01:14:01.886] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-09-14 01:14:01.888] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20\nallowedIn: 12\nMax Junction ID: 70\nseen.size():569 kmerInfo.size():71\napproximateContigTotalLength: 17465\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 24 element count: 19592 complex nodes: 0\n# of ones in rank vector: 23\n[2024-09-14 01:14:01.952] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-09-14 01:14:01.952] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 19592\n-----------------------------------------\n| Loading contigs | Time = 1.8348 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading contig boundaries | Time = 1.0511 ms\n-----------------------------------------\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n23\n[2024-09-14 01:14:01.955] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-09-14 01:14:01.955] [puff::index::jointLog] [info] contig count for validation: 23\n[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] Total # of Contigs : 23\n[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] Total # of numerical Contigs : 23\n[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] Total # of contig vec entries: 36\n[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] bits per offset entry 6\n[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] Done constructing the contig vector. 24\n[2024-09-14 01:14:01.970] [puff::index::jointLog] [info] # segments = 23\n[2024-09-14 01:14:01.970] [puff::index::jointLog] [info] total length = 19592\n[2024-09-14 01:14:01.970] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] positional integer width = 15\n[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] seqSize = 19592\n[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] rankSize = 19592\n[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] num keys = 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min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-09-14 01:14:02.084] [puff::index::jointLog] [info] mphf size = 0.0125198 MB\n[2024-09-14 01:14:02.084] [puff::index::jointLog] [info] chunk size = 9796\n[2024-09-14 01:14:02.084] [puff::index::jointLog] [info] chunk 0 = [0, 9796)\n[2024-09-14 01:14:02.084] [puff::index::jointLog] [info] chunk 1 = [9796, 19562)\n[2024-09-14 01:14:02.085] [puff::index::jointLog] [info] finished populating pos vector\n[2024-09-14 01:14:02.085] [puff::index::jointLog] [info] writing index components\n[2024-09-14 01:14:02.100] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-09-14 01:14:02.107] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n### salmon (selective-alignment-based) v1.3.0\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { U }\n### [ unmatedReads ] => { ./single.fasta }\n### [ threads ] => { 6 }\n### [ incompatPrior ] => { 0.0 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 100 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 1e-05 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n[2024-09-14 01:14:02.202] [jointLog] [info] setting maxHashResizeThreads to 6\n[2024-09-14 01:14:02.202] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-09-14 01:14:02.202] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-09-14 01:14:02.202] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.\n[2024-09-14 01:14:02.202] [jointLog] [info] parsing read library format\n[2024-09-14 01:14:02.202] [jointLog] [info] There is 1 library.\n-----------------------------------------\n| Loading contig table | Time = 1.1905 ms\n-----------------------------------------\nsize = 24\n-----------------------------------------\n| Loading contig offsets | Time = 1.7182 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 564.82 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 1.2042 ms\n-----------------------------------------\nsize = 19592\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 1.1029 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading sequence | Time = 952.18 us\n-----------------------------------------\nsize = 18902\n-----------------------------------------\n| Loading positions | Time = 1.5979 ms\n-----------------------------------------\nsize = 28562\n-----------------------------------------\n| Loading reference sequence | Time = 803.94 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 595.88 us\n-----------------------------------------\n[2024-09-14 01:14:02.288] [jointLog] [info] Loading pufferfish index\n[2024-09-14 01:14:02.289] [jointLog] [info] Loading dense pufferfish index.\n[2024-09-14 01:14:02.301] [jointLog] [info] done\n[2024-09-14 01:14:02.301] [jointLog] [info] Index contained 15 targets\n[2024-09-14 01:14:02.301] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2024-09-14 01:14:02.348] [jointLog] [info] Computed 15 rich equivalence classes for further processing\n[2024-09-14 01:14:02.348] [jointLog] [info] Counted 15 total reads in the equivalence classes \n[2024-09-14 01:14:02.349] [jointLog] [info] Number of mappings discarded because of alignment score : 5\n[2024-09-14 01:14:02.349] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2024-09-14 01:14:02.349] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-09-14 01:14:02.349] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2024-09-14 01:14:02.350] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2024-09-14 01:14:02.350] [jointLog] [info] Mapping rate = 100%\n\n[2024-09-14 01:14:02.350] [jointLog] [info] finished quantifyLibrary()\n[2024-09-14 01:14:02.354] [jointLog] [info] Starting optimizer\n[2024-09-14 01:14:02.355] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2024-09-14 01:14:02.355] [jointLog] [info] iteration = 0 | max rel diff. = 0\n[2024-09-14 01:14:02.356] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2024-09-14 01:14:02.357] [jointLog] [info] Finished optimizer\n[2024-09-14 01:14:02.357] [jointLog] [info] writing output \n\n[2024-09-14 01:14:02.362] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 14\nFalse junctions count = 18\nHash table size = 32\nCandidate marks count = 55\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 51\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 14\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 105024 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-14 01:14:03", "plugin": "core", "name": "end_epoch", "raw_value": "1726276443.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:14:01", "plugin": "core", "name": "start_epoch", "raw_value": "1726276441.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}]}, "status": "success"}}, {"id": "salmon/1.3.0+galaxy1-2", "has_data": true, "data": {"tool_id": "salmon", "tool_version": "1.3.0+galaxy1", "test_index": 2, "time_seconds": 27.406590223312378, "inputs": {"quant_type|refTranscriptSource|s_index|fasta": {"src": "hda", "id": "d9a4dce5c32f8400"}, "quant_type|refTranscriptSource|TranscriptSource": "history", "quant_type|qtype": "reads"}, "job": {"model_class": "Job", "id": "7f019bb254bd9239", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:14:39.710818", "create_time": "2024-09-14T01:14:27.909771", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-r2gwj", "command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/0/8/d/dataset_08d44003-a573-41ec-b62e-688862d1ed8f.dat' && ln -s /galaxy/server/database/objects/0/8/d/dataset_08d44003-a573-41ec-b62e-688862d1ed8f.dat ./single.fasta && salmon quant --index './index' --libType U --unmatedReads ./single.fasta --threads \"${GALAXY_SLOTS:-4}\" --incompatPrior '0.0' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '100' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '1e-05' -o ./output", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"biasSpeedSamp\": \"5\", \"bootstrapReproject\": false, \"dumpEq\": false, \"dumpEqWeights\": false, \"fldMax\": \"1000\", \"fldMean\": \"250\", \"fldSD\": \"25\", \"forgettingFactor\": \"0.65\", \"initUniform\": false, \"maxReadOcc\": \"100\", \"minAssignedFrags\": \"\", \"noBiasLengthThreshold\": false, \"noEffectiveLengthCorrection\": false, \"noFragLengthDist\": false, \"noGammaDraw\": false, \"noLengthCorrection\": false, \"numAuxModelSamples\": \"5000000\", \"numBiasSamples\": \"2000000\", \"numBootstraps\": \"0\", \"numGibbsSamples\": \"0\", \"numPreAuxModelSamples\": \"5000\", \"perTranscriptPrior\": false, \"rangeFactorizationBins\": \"0\", \"sigDigits\": \"3\", \"skipQuant\": false, \"thinningFactor\": \"16\", \"useEM\": false, \"vbPrior\": \"1e-05\", \"writeOrphanLinks\": false, \"writeUnmappedNames\": false}", "meta": "false", "incompatPrior": "\"0.0\"", "gcBias": "false", "seqBias": "false", "geneMap": null, "quant_type": "{\"__current_case__\": 0, \"consensusSlack\": \"0\", \"consistentHits\": false, \"discardOrphansQuasi\": false, \"dovetail\": false, \"input\": {\"single_or_paired\": {\"__current_case__\": 0, \"input_singles\": {\"values\": [{\"id\": 136, \"src\": \"hda\"}]}, \"single_or_paired_opts\": \"single\", \"strandedness\": \"U\"}}, \"qtype\": \"reads\", \"quasiCoverage\": \"\", \"recoverOrphans\": false, \"refTranscriptSource\": {\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 136, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}, \"type\": \"quasi\", \"validmap\": {\"__current_case__\": 1, \"validateMappings\": false}, \"writeMappings\": false}"}, "inputs": {"quant_type|refTranscriptSource|s_index|fasta": {"id": "d9a4dce5c32f8400", "src": "hda", "uuid": "08d44003-a573-41ec-b62e-688862d1ed8f"}, "quant_type|input|single_or_paired|input_singles": {"id": "d9a4dce5c32f8400", "src": "hda", "uuid": "08d44003-a573-41ec-b62e-688862d1ed8f"}}, "outputs": {"output_quant": {"id": "11776b2b82446576", "src": "hda", "uuid": "a0f7eb43-1680-46d0-bfec-ba26c3659da1"}}, "output_collections": {}, "tool_stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 14\nFalse junctions count = 18\nHash table size = 32\nCandidate marks count = 55\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 51\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 14\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 105024 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "tool_stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n[2024-09-14 01:14:30.463] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-09-14 01:14:30.463] [jLog] [info] building index\nout : ./index\n[2024-09-14 01:14:30.465] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-09-14 01:14:30.473] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-09-14 01:14:30.473] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 15 cleaned references\n[2024-09-14 01:14:30.488] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-09-14 01:14:30.490] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20\nallowedIn: 12\nMax Junction ID: 70\nseen.size():569 kmerInfo.size():71\napproximateContigTotalLength: 17465\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 24 element count: 19592 complex nodes: 0\n# of ones in rank vector: 23\n[2024-09-14 01:14:30.555] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-09-14 01:14:30.555] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 19592\n-----------------------------------------\n| Loading contigs | Time = 1.3885 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading contig boundaries | Time = 995.27 us\n-----------------------------------------\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n23\n[2024-09-14 01:14:30.558] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-09-14 01:14:30.558] [puff::index::jointLog] [info] contig count for validation: 23\n[2024-09-14 01:14:30.558] [puff::index::jointLog] [info] Total # of Contigs : 23\n[2024-09-14 01:14:30.558] [puff::index::jointLog] [info] Total # of numerical Contigs : 23\n[2024-09-14 01:14:30.559] [puff::index::jointLog] [info] Total # of contig vec entries: 36\n[2024-09-14 01:14:30.559] [puff::index::jointLog] [info] bits per offset entry 6\n[2024-09-14 01:14:30.559] [puff::index::jointLog] [info] Done constructing the contig vector. 24\n[2024-09-14 01:14:30.570] [puff::index::jointLog] [info] # segments = 23\n[2024-09-14 01:14:30.570] [puff::index::jointLog] [info] total length = 19592\n[2024-09-14 01:14:30.570] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] positional integer width = 15\n[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] seqSize = 19592\n[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] rankSize = 19592\n[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] num keys = 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elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-09-14 01:14:30.661] [puff::index::jointLog] [info] mphf size = 0.0125198 MB\n[2024-09-14 01:14:30.661] [puff::index::jointLog] [info] chunk size = 9796\n[2024-09-14 01:14:30.661] [puff::index::jointLog] [info] chunk 0 = [0, 9796)\n[2024-09-14 01:14:30.661] [puff::index::jointLog] [info] chunk 1 = [9796, 19562)\n[2024-09-14 01:14:30.662] [puff::index::jointLog] [info] finished populating pos vector\n[2024-09-14 01:14:30.662] [puff::index::jointLog] [info] writing index components\n[2024-09-14 01:14:30.675] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-09-14 01:14:30.681] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n### salmon (selective-alignment-based) v1.3.0\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { U }\n### [ unmatedReads ] => { ./single.fasta }\n### [ threads ] => { 6 }\n### [ incompatPrior ] => { 0.0 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 100 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 1e-05 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n[2024-09-14 01:14:30.759] [jointLog] [info] setting maxHashResizeThreads to 6\n[2024-09-14 01:14:30.759] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-09-14 01:14:30.759] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-09-14 01:14:30.759] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.\n[2024-09-14 01:14:30.759] [jointLog] [info] parsing read library format\n[2024-09-14 01:14:30.759] [jointLog] [info] There is 1 library.\n-----------------------------------------\n| Loading contig table | Time = 1.2042 ms\n-----------------------------------------\nsize = 24\n-----------------------------------------\n| Loading contig offsets | Time = 1.5305 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 697.75 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 505.56 us\n-----------------------------------------\nsize = 19592\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 908.85 us\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading sequence | Time = 1.0946 ms\n-----------------------------------------\nsize = 18902\n-----------------------------------------\n| Loading positions | Time = 1.4588 ms\n-----------------------------------------\nsize = 28562\n-----------------------------------------\n| Loading reference sequence | Time = 1.0765 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 668.87 us\n-----------------------------------------\n[2024-09-14 01:14:30.845] [jointLog] [info] Loading pufferfish index\n[2024-09-14 01:14:30.847] [jointLog] [info] Loading dense pufferfish index.\n[2024-09-14 01:14:30.858] [jointLog] [info] done\n[2024-09-14 01:14:30.858] [jointLog] [info] Index contained 15 targets\n[2024-09-14 01:14:30.858] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2024-09-14 01:14:30.905] [jointLog] [info] Computed 15 rich equivalence classes for further processing\n[2024-09-14 01:14:30.905] [jointLog] [info] Counted 15 total reads in the equivalence classes \n[2024-09-14 01:14:30.906] [jointLog] [info] Number of mappings discarded because of alignment score : 5\n[2024-09-14 01:14:30.906] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2024-09-14 01:14:30.906] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-09-14 01:14:30.906] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2024-09-14 01:14:30.906] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2024-09-14 01:14:30.906] [jointLog] [info] Mapping rate = 100%\n\n[2024-09-14 01:14:30.906] [jointLog] [info] finished quantifyLibrary()\n[2024-09-14 01:14:30.911] [jointLog] [info] Starting optimizer\n[2024-09-14 01:14:30.911] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2024-09-14 01:14:30.911] [jointLog] [info] iteration = 0 | max rel diff. = 0\n[2024-09-14 01:14:30.913] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2024-09-14 01:14:30.913] [jointLog] [info] Finished optimizer\n[2024-09-14 01:14:30.913] [jointLog] [info] writing output \n\n[2024-09-14 01:14:30.918] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "job_stdout": "", "job_stderr": "", "stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n[2024-09-14 01:14:30.463] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-09-14 01:14:30.463] [jLog] [info] building index\nout : ./index\n[2024-09-14 01:14:30.465] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-09-14 01:14:30.473] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-09-14 01:14:30.473] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 15 cleaned references\n[2024-09-14 01:14:30.488] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-09-14 01:14:30.490] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20\nallowedIn: 12\nMax Junction ID: 70\nseen.size():569 kmerInfo.size():71\napproximateContigTotalLength: 17465\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 24 element count: 19592 complex nodes: 0\n# of ones in rank vector: 23\n[2024-09-14 01:14:30.555] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-09-14 01:14:30.555] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 19592\n-----------------------------------------\n| Loading contigs | Time = 1.3885 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading contig boundaries | Time = 995.27 us\n-----------------------------------------\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n23\n[2024-09-14 01:14:30.558] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-09-14 01:14:30.558] [puff::index::jointLog] [info] contig count for validation: 23\n[2024-09-14 01:14:30.558] [puff::index::jointLog] [info] Total # of Contigs : 23\n[2024-09-14 01:14:30.558] [puff::index::jointLog] [info] Total # of numerical Contigs : 23\n[2024-09-14 01:14:30.559] [puff::index::jointLog] [info] Total # of contig vec entries: 36\n[2024-09-14 01:14:30.559] [puff::index::jointLog] [info] bits per offset entry 6\n[2024-09-14 01:14:30.559] [puff::index::jointLog] [info] Done constructing the contig vector. 24\n[2024-09-14 01:14:30.570] [puff::index::jointLog] [info] # segments = 23\n[2024-09-14 01:14:30.570] [puff::index::jointLog] [info] total length = 19592\n[2024-09-14 01:14:30.570] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] positional integer width = 15\n[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] seqSize = 19592\n[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] rankSize = 19592\n[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] num keys = 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elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-09-14 01:14:30.661] [puff::index::jointLog] [info] mphf size = 0.0125198 MB\n[2024-09-14 01:14:30.661] [puff::index::jointLog] [info] chunk size = 9796\n[2024-09-14 01:14:30.661] [puff::index::jointLog] [info] chunk 0 = [0, 9796)\n[2024-09-14 01:14:30.661] [puff::index::jointLog] [info] chunk 1 = [9796, 19562)\n[2024-09-14 01:14:30.662] [puff::index::jointLog] [info] finished populating pos vector\n[2024-09-14 01:14:30.662] [puff::index::jointLog] [info] writing index components\n[2024-09-14 01:14:30.675] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-09-14 01:14:30.681] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n### salmon (selective-alignment-based) v1.3.0\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { U }\n### [ unmatedReads ] => { ./single.fasta }\n### [ threads ] => { 6 }\n### [ incompatPrior ] => { 0.0 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 100 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 1e-05 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n[2024-09-14 01:14:30.759] [jointLog] [info] setting maxHashResizeThreads to 6\n[2024-09-14 01:14:30.759] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-09-14 01:14:30.759] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-09-14 01:14:30.759] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.\n[2024-09-14 01:14:30.759] [jointLog] [info] parsing read library format\n[2024-09-14 01:14:30.759] [jointLog] [info] There is 1 library.\n-----------------------------------------\n| Loading contig table | Time = 1.2042 ms\n-----------------------------------------\nsize = 24\n-----------------------------------------\n| Loading contig offsets | Time = 1.5305 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 697.75 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 505.56 us\n-----------------------------------------\nsize = 19592\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 908.85 us\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading sequence | Time = 1.0946 ms\n-----------------------------------------\nsize = 18902\n-----------------------------------------\n| Loading positions | Time = 1.4588 ms\n-----------------------------------------\nsize = 28562\n-----------------------------------------\n| Loading reference sequence | Time = 1.0765 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 668.87 us\n-----------------------------------------\n[2024-09-14 01:14:30.845] [jointLog] [info] Loading pufferfish index\n[2024-09-14 01:14:30.847] [jointLog] [info] Loading dense pufferfish index.\n[2024-09-14 01:14:30.858] [jointLog] [info] done\n[2024-09-14 01:14:30.858] [jointLog] [info] Index contained 15 targets\n[2024-09-14 01:14:30.858] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2024-09-14 01:14:30.905] [jointLog] [info] Computed 15 rich equivalence classes for further processing\n[2024-09-14 01:14:30.905] [jointLog] [info] Counted 15 total reads in the equivalence classes \n[2024-09-14 01:14:30.906] [jointLog] [info] Number of mappings discarded because of alignment score : 5\n[2024-09-14 01:14:30.906] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2024-09-14 01:14:30.906] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-09-14 01:14:30.906] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2024-09-14 01:14:30.906] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2024-09-14 01:14:30.906] [jointLog] [info] Mapping rate = 100%\n\n[2024-09-14 01:14:30.906] [jointLog] [info] finished quantifyLibrary()\n[2024-09-14 01:14:30.911] [jointLog] [info] Starting optimizer\n[2024-09-14 01:14:30.911] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2024-09-14 01:14:30.911] [jointLog] [info] iteration = 0 | max rel diff. = 0\n[2024-09-14 01:14:30.913] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2024-09-14 01:14:30.913] [jointLog] [info] Finished optimizer\n[2024-09-14 01:14:30.913] [jointLog] [info] writing output \n\n[2024-09-14 01:14:30.918] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 14\nFalse junctions count = 18\nHash table size = 32\nCandidate marks count = 55\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 51\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 14\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 105024 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-14 01:14:31", "plugin": "core", "name": "end_epoch", "raw_value": "1726276471.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:14:30", "plugin": "core", "name": "start_epoch", "raw_value": "1726276470.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}]}, "status": "success"}}, {"id": "salmon/1.3.0+galaxy1-3", "has_data": true, "data": {"tool_id": "salmon", "tool_version": "1.3.0+galaxy1", "test_index": 3, "time_seconds": 32.30054974555969, "inputs": {"quant_type|afile": {"src": "hda", "id": "483e03d1592daa99"}, "quant_type|transcript": {"src": "hda", "id": "0ace53d3c68a37f6"}, "quant_type|noErrorModel": true, "quant_type|numErrorBins": "5", "quant_type|sampleOut": true, "quant_type|sampleUnaligned": true, "quant_type|qtype": "alignment"}, "job": {"model_class": "Job", "id": "52d5cbcb026d8518", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:15:11.675578", "create_time": "2024-09-14T01:14:58.676001", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-ckb7q", "command_line": "salmon quant -t '/galaxy/server/database/objects/3/f/9/dataset_3f98742b-13bf-4a63-b43c-e12943fc60b3.dat' -l 'U' -a '/galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat' --threads \"${GALAXY_SLOTS:-4}\" --noErrorModel --numErrorBins '5' --sampleOut --sampleUnaligned --incompatPrior '0.0' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '100' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '1e-05' -o ./output && samtools sort -@ ${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam ./output/postSample.bam", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"biasSpeedSamp\": \"5\", \"bootstrapReproject\": false, \"dumpEq\": false, \"dumpEqWeights\": false, \"fldMax\": \"1000\", \"fldMean\": \"250\", \"fldSD\": \"25\", \"forgettingFactor\": \"0.65\", \"initUniform\": false, \"maxReadOcc\": \"100\", \"minAssignedFrags\": \"\", \"noBiasLengthThreshold\": false, \"noEffectiveLengthCorrection\": false, \"noFragLengthDist\": false, \"noGammaDraw\": false, \"noLengthCorrection\": false, \"numAuxModelSamples\": \"5000000\", \"numBiasSamples\": \"2000000\", \"numBootstraps\": \"0\", \"numGibbsSamples\": \"0\", \"numPreAuxModelSamples\": \"5000\", \"perTranscriptPrior\": false, \"rangeFactorizationBins\": \"0\", \"sigDigits\": \"3\", \"skipQuant\": false, \"thinningFactor\": \"16\", \"useEM\": false, \"vbPrior\": \"1e-05\", \"writeOrphanLinks\": false, \"writeUnmappedNames\": false}", "meta": "false", "incompatPrior": "\"0.0\"", "gcBias": "false", "seqBias": "false", "geneMap": null, "quant_type": "{\"__current_case__\": 1, \"afile\": {\"values\": [{\"id\": 138, \"src\": \"hda\"}]}, \"discardOrphans\": false, \"gencode\": false, \"noErrorModel\": true, \"numErrorBins\": \"5\", \"qtype\": \"alignment\", \"sampleOut\": true, \"sampleUnaligned\": true, \"strandedness\": \"U\", \"transcript\": {\"values\": [{\"id\": 139, \"src\": \"hda\"}]}}"}, "inputs": {"quant_type|afile": {"id": "483e03d1592daa99", "src": "hda", "uuid": "cc6c1385-feae-4b8f-9391-4715d9c69c89"}, "quant_type|transcript": {"id": "0ace53d3c68a37f6", "src": "hda", "uuid": "3f98742b-13bf-4a63-b43c-e12943fc60b3"}}, "outputs": {"output_quant": {"id": "d9070c6d9b86ff3b", "src": "hda", "uuid": "972ea182-a315-4243-a8ed-f418494b7f6b"}, "postSample": {"id": "849c12e90d2d3fd6", "src": "hda", "uuid": "3650dd27-e490-4cb2-8a06-c0979282d02b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n# salmon (alignment-based) v1.3.0\n# [ program ] => salmon \n# [ command ] => quant \n# [ targets ] => { /galaxy/server/database/objects/3/f/9/dataset_3f98742b-13bf-4a63-b43c-e12943fc60b3.dat }\n# [ libType ] => { U }\n# [ alignments ] => { /galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat }\n# [ threads ] => { 6 }\n# [ noErrorModel ] => { }\n# [ numErrorBins ] => { 5 }\n# [ sampleOut ] => { }\n# [ sampleUnaligned ] => { }\n# [ incompatPrior ] => { 0.0 }\n# [ biasSpeedSamp ] => { 5 }\n# [ fldMax ] => { 1000 }\n# [ fldMean ] => { 250 }\n# [ fldSD ] => { 25 }\n# [ forgettingFactor ] => { 0.65 }\n# [ maxReadOcc ] => { 100 }\n# [ numBiasSamples ] => { 2000000 }\n# [ numAuxModelSamples ] => { 5000000 }\n# [ numPreAuxModelSamples ] => { 5000 }\n# [ numGibbsSamples ] => { 0 }\n# [ numBootstraps ] => { 0 }\n# [ thinningFactor ] => { 16 }\n# [ sigDigits ] => { 3 }\n# [ vbPrior ] => { 1e-05 }\n# [ output ] => { ./output }\nLogs will be written to ./output/logs\n[2024-09-14 01:15:00.963] [jointLog] [info] setting maxHashResizeThreads to 6\n[2024-09-14 01:15:00.963] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\nLibrary format { type:single end, relative orientation:none, strandedness:unstranded }\n[2024-09-14 01:15:00.965] [jointLog] [info] numQuantThreads = 3\nparseThreads = 3\nChecking that provided alignment files have consistent headers . . . done\nPopulating targets from aln = \"/galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat\", fasta = \"/galaxy/server/database/objects/3/f/9/dataset_3f98742b-13bf-4a63-b43c-e12943fc60b3.dat\" . . .done\n\n\n\n\n\r\r\u001b[0;32mprocessed\u001b[0;31m 0 \u001b[0;32mreads in current round\u001b[0;0m\r\r\u001b[0;32mprocessed\u001b[0;31m 28503 \u001b[0;32mreads in current round\u001b[0;0m\n\r\rkilling thread 0 . . . done\r\rkilling thread 1 . . . done\r\rkilling thread 2 . . . done\n\n# observed = 28503 / # required = 50000000\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n\n\n\nResetting BAMQueue from file(s) [ \"/galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat\" ] . . . done\n\r\r\u001b[32mprocessed\u001b[31m 0 \u001b[32mreads\u001b[0m\nkilling thread 0 . . . done\r\rkilling thread 1 . . . done\r\rkilling thread 2 . . . done\r\r\n# observed = 28503 mapped fragments.\u001b[F\u001b[F\u001b[F\u001b[FWaiting on output thread\ndone\n\n\n\n\n\nFreeing memory used by read queue . . . \nJoined parsing thread . . . \"/galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat\" \nClosed all files . . . [2024-09-14 01:15:01.340] [jointLog] [info] replaced 0 non-ACGT nucleotides with random nucleotides\n[2024-09-14 01:15:01.515] [jointLog] [info] \n\n\nCompleted first pass through the alignment file.\nTotal # of mapped reads : 28503\n# of uniquely mapped reads : 28502\n# ambiguously mapped reads : 1\n\n\n\n[2024-09-14 01:15:01.519] [jointLog] [info] Computed 18 rich equivalence classes for further processing\n[2024-09-14 01:15:01.519] [jointLog] [info] Counted 28503 total reads in the equivalence classes \n[2024-09-14 01:15:01.519] [jointLog] [warning] Only 28503 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2024-09-14 01:15:01.521] [jointLog] [info] starting optimizer\n[2024-09-14 01:15:01.521] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2024-09-14 01:15:01.521] [jointLog] [info] iteration = 0 | max rel diff. = 21.8815\n[2024-09-14 01:15:01.523] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2024-09-14 01:15:01.523] [jointLog] [info] finished optimizer\n[2024-09-14 01:15:01.523] [jointLog] [info] writing output\n[2024-09-14 01:15:01.528] [jointLog] [info] Sampling alignments; outputting results to ./output/postSample.bam\n\n\nEmptied frag queue. . . \nEmptied Alignemnt Group Pool. . \nEmptied Alignment Group Queue. . . done\n[bam_sort_core] merging from 0 files and 6 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n# salmon (alignment-based) v1.3.0\n# [ program ] => salmon \n# [ command ] => quant \n# [ targets ] => { /galaxy/server/database/objects/3/f/9/dataset_3f98742b-13bf-4a63-b43c-e12943fc60b3.dat }\n# [ libType ] => { U }\n# [ alignments ] => { /galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat }\n# [ threads ] => { 6 }\n# [ noErrorModel ] => { }\n# [ numErrorBins ] => { 5 }\n# [ sampleOut ] => { }\n# [ sampleUnaligned ] => { }\n# [ incompatPrior ] => { 0.0 }\n# [ biasSpeedSamp ] => { 5 }\n# [ fldMax ] => { 1000 }\n# [ fldMean ] => { 250 }\n# [ fldSD ] => { 25 }\n# [ forgettingFactor ] => { 0.65 }\n# [ maxReadOcc ] => { 100 }\n# [ numBiasSamples ] => { 2000000 }\n# [ numAuxModelSamples ] => { 5000000 }\n# [ numPreAuxModelSamples ] => { 5000 }\n# [ numGibbsSamples ] => { 0 }\n# [ numBootstraps ] => { 0 }\n# [ thinningFactor ] => { 16 }\n# [ sigDigits ] => { 3 }\n# [ vbPrior ] => { 1e-05 }\n# [ output ] => { ./output }\nLogs will be written to ./output/logs\n[2024-09-14 01:15:00.963] [jointLog] [info] setting maxHashResizeThreads to 6\n[2024-09-14 01:15:00.963] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\nLibrary format { type:single end, relative orientation:none, strandedness:unstranded }\n[2024-09-14 01:15:00.965] [jointLog] [info] numQuantThreads = 3\nparseThreads = 3\nChecking that provided alignment files have consistent headers . . . done\nPopulating targets from aln = \"/galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat\", fasta = \"/galaxy/server/database/objects/3/f/9/dataset_3f98742b-13bf-4a63-b43c-e12943fc60b3.dat\" . . .done\n\n\n\n\n\r\r\u001b[0;32mprocessed\u001b[0;31m 0 \u001b[0;32mreads in current round\u001b[0;0m\r\r\u001b[0;32mprocessed\u001b[0;31m 28503 \u001b[0;32mreads in current round\u001b[0;0m\n\r\rkilling thread 0 . . . done\r\rkilling thread 1 . . . done\r\rkilling thread 2 . . . done\n\n# observed = 28503 / # required = 50000000\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n\n\n\nResetting BAMQueue from file(s) [ \"/galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat\" ] . . . done\n\r\r\u001b[32mprocessed\u001b[31m 0 \u001b[32mreads\u001b[0m\nkilling thread 0 . . . done\r\rkilling thread 1 . . . done\r\rkilling thread 2 . . . done\r\r\n# observed = 28503 mapped fragments.\u001b[F\u001b[F\u001b[F\u001b[FWaiting on output thread\ndone\n\n\n\n\n\nFreeing memory used by read queue . . . \nJoined parsing thread . . . \"/galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat\" \nClosed all files . . . [2024-09-14 01:15:01.340] [jointLog] [info] replaced 0 non-ACGT nucleotides with random nucleotides\n[2024-09-14 01:15:01.515] [jointLog] [info] \n\n\nCompleted first pass through the alignment file.\nTotal # of mapped reads : 28503\n# of uniquely mapped reads : 28502\n# ambiguously mapped reads : 1\n\n\n\n[2024-09-14 01:15:01.519] [jointLog] [info] Computed 18 rich equivalence classes for further processing\n[2024-09-14 01:15:01.519] [jointLog] [info] Counted 28503 total reads in the equivalence classes \n[2024-09-14 01:15:01.519] [jointLog] [warning] Only 28503 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2024-09-14 01:15:01.521] [jointLog] [info] starting optimizer\n[2024-09-14 01:15:01.521] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2024-09-14 01:15:01.521] [jointLog] [info] iteration = 0 | max rel diff. = 21.8815\n[2024-09-14 01:15:01.523] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2024-09-14 01:15:01.523] [jointLog] [info] finished optimizer\n[2024-09-14 01:15:01.523] [jointLog] [info] writing output\n[2024-09-14 01:15:01.528] [jointLog] [info] Sampling alignments; outputting results to ./output/postSample.bam\n\n\nEmptied frag queue. . . \nEmptied Alignemnt Group Pool. . \nEmptied Alignment Group Queue. . . done\n[bam_sort_core] merging from 0 files and 6 in-memory blocks...\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-14 01:15:02", "plugin": "core", "name": "end_epoch", "raw_value": "1726276502.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:15:00", "plugin": "core", "name": "start_epoch", "raw_value": "1726276500.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}]}, "output_problems": ["Output postSample: different than expected, difference (using diff):\n( /tmp/local_bam_converted_to_sam_5ygtg3m0.sam v. /tmp/history_bam_converted_to_sam_5bnsu6xc.sam )\n--- local_file\n+++ history_data\n@@ -1,4 +1,6 @@\n @HD\tVN:1.0\tSO:coordinate\n+@PG\tID:rapmap\tPN:rapmap\tVN:0.6.0\n+@PG\tID:samtools\tPN:samtools\tPP:rapmap\tVN:1.10\tCL:samtools sort -@ 6 --output-fmt=BAM -o ./output/bamout.bam ./output/postSample.bam\n @SQ\tSN:NM_001168316\tLN:2283\n @SQ\tSN:NM_174914\tLN:2385\n @SQ\tSN:NR_031764\tLN:1853\n@@ -14,66 +16,136 @@\n @SQ\tSN:NM_153693\tLN:2072\n @SQ\tSN:NM_173860\tLN:849\n @SQ\tSN:NR_003084\tLN:1640\n-@PG\tID:rapmap\tPN:rapmap\tVN:0.6.0\n-@PG\tID:samtools\tPN:samtools\tPP:rapmap\tVN:1.16.1\tCL:samtools sort -@ 1 --output-fmt=BAM -o ./output/bamout.bam ./output/postSample.bam\n+1811:NM_174914:0:188\t99\tNM_001168316\t1\t1\t50M\t=\t139\t188\tTTAGTGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAA\t*\tNH:i:3\tHI:i:1\tAS:i:0\n+3775:NM_174914:0:140\t99\tNM_001168316\t1\t1\t50M\t=\t91\t140\tTTAGTGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAA\t*\tNH:i:3\tHI:i:1\tAS:i:0\n 8380:NM_174914:0:170\t163\tNM_001168316\t1\t1\t50M\t=\t121\t170\tTTAGTGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAA\t*\tNH:i:3\tHI:i:1\tAS:i:0\n+567:NM_174914:5:165\t99\tNM_001168316\t6\t1\t50M\t=\t121\t165\tGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGG\t*\tNH:i:3\tHI:i:1\tAS:i:0\n 2546:NM_174914:6:160\t163\tNM_001168316\t7\t1\t50M\t=\t117\t160\tAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGA\t*\tNH:i:3\tHI:i:1\tAS:i:0\n+4806:NR_031764:7:194\t99\tNM_001168316\t8\t1\t50M\t=\t152\t194\tGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAA\t*\tNH:i:3\tHI:i:1\tAS:i:0\n+2590:NR_031764:8:152\t99\tNM_001168316\t9\t1\t50M\t=\t111\t152\tGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAA\t*\tNH:i:3\tHI:i:1\tAS:i:0\n+1161:NM_174914:9:183\t99\tNM_001168316\t10\t1\t50M\t=\t143\t183\tTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAAC\t*\tNH:i:3\tHI:i:1\tAS:i:0\n+1332:NM_174914:10:177\t99\tNM_001168316\t11\t1\t50M\t=\t138\t177\tTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAACC\t*\tNH:i:3\tHI:i:1\tAS:i:0\n+6621:NM_174914:10:179\t99\tNM_001168316\t11\t1\t50M\t=\t140\t179\tTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAACC\t*\tNH:i:3\tHI:i:1\tAS:i:0\n********\n*SNIP *\n********\n+9853:NM_018953:1427:182\t355\tNR_003084\t1456\t1\t50M\t=\t1588\t182\tCAACTAGTGGGGTTTCCTGGCACTGGACCCCAGCAAGTGGTCCTAGAGGC\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+7857:NM_018953:1428:165\t419\tNR_003084\t1457\t1\t50M\t=\t1572\t165\tAACTAGTGGGGTTTCCTGGCACTGGACCCCAGCAAGTGGTCCTAGAGGCC\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+3858:NM_018953:1305:183\t339\tNR_003084\t1467\t1\t50M\t=\t1334\t-183\tGTTTCCTGGCACTGGACCCCAGCAAGTGGTCCTAGAGGCCCTTTGCTGTC\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+8186:NM_018953:1442:153\t355\tNR_003084\t1471\t1\t50M\t=\t1574\t153\tCCTGGCACTGGACCCCAGCAAGTGGTCCTAGAGGCCCTTTGCTGTCCCAT\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+3225:NM_018953:1324:177\t403\tNR_003084\t1480\t1\t50M\t=\t1353\t-177\tGGACCCCAGCAAGTGGTCCTAGAGGCCCTTTGCTGTCCCATAGTCCCTGC\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+9380:NM_018953:1348:155\t403\tNR_003084\t1482\t1\t50M\t=\t1377\t-155\tACCCCAGCAAGTGGTCCTAGAGGCCCTTTGCTGTCCCATAGTCCCTGCCA\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+6585:NM_018953:1338:169\t403\tNR_003084\t1486\t1\t50M\t=\t1367\t-169\tCAGCAAGTGGTCCTAGAGGCCCTTTGCTGTCCCATAGTCCCTGCCACGAA\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+6863:NM_018953:1319:193\t339\tNR_003084\t1491\t1\t50M\t=\t1348\t-193\tAGTGGTCCTAGAGGCCCTTTGCTGTCCCATAGTCCCTGCCACGAATTTCT\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+9258:NM_018953:1324:191\t403\tNR_003084\t1494\t1\t50M\t=\t1353\t-191\tGGTCCTAGAGGCCCTTTGCTGTCCCATAGTCCCTGCCACGAATTTCTGTG\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+4115:NM_018953:1339:179\t403\tNR_003084\t1497\t1\t50M\t=\t1368\t-179\tCCTAGAGGCCCTTTGCTGTCCCATAGTCCCTGCCACGAATTTCTGTGCCC\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+6135:NM_018953:1469:91\t355\tNR_003084\t1498\t1\t50M\t=\t1539\t91\tCTAGAGGCCCTTTGCTGTCCCATAGTCCCTGCCACGAATTTCTGTGCCCT\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+9697:NM_018953:1346:184\t339\tNR_003084\t1509\t1\t50M\t=\t1375\t-184\tTTGCTGTCCCATAGTCCCTGCCACGAATTTCTGTGCCCTCCTGACCCATT\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+434:NM_018953:1346:194\t339\tNR_003084\t1519\t1\t50M\t=\t1375\t-194\tATAGTCCCTGCCACGAATTTCTGTGCCCTCCTGACCCATTGCTGTTGTCC\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+9192:NM_018953:1402:146\t403\tNR_003084\t1527\t1\t50M\t=\t1431\t-146\tTGCCACGAATTTCTGTGCCCTCCTGACCCATTGCTGTTGTCCAACTATTT\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+5171:NM_018953:1389:171\t339\tNR_003084\t1539\t1\t50M\t=\t1418\t-171\tCTGTGCCCTCCTGACCCATTGCTGTTGTCCAACTATTTATTGACTCTGGG\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+6135:NM_018953:1469:91\t403\tNR_003084\t1539\t1\t50M\t=\t1498\t-91\tCTGTGCCCTCCTGACCCATTGCTGTTGTCCAACTATTTATTGACTCTGGG\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+9690:NM_018953:1392:171\t339\tNR_003084\t1542\t1\t50M\t=\t1421\t-171\tTGCCCTCCTGACCCATTGCTGTTGTCCAACTATTTATTGACTCTGGGTCC\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+1465:NM_018953:1400:169\t339\tNR_003084\t1548\t1\t50M\t=\t1429\t-169\tCCTGACCCATTGCTGTTGTCCAACTATTTATTGACTCTGGGTCCTTCCTG\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+3052:NM_018953:1396:175\t339\tNR_003084\t1550\t1\t50M\t=\t1425\t-175\tTGACCCATTGCTGTTGTCCAACTATTTATTGACTCTGGGTCCTTCCTGAA\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+381:NM_018953:1382:192\t339\tNR_003084\t1553\t1\t50M\t=\t1411\t-192\tCCCATTGCTGTTGTCCAACTATTTATTGACTCTGGGTCCTTCCTGAAACT\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+7857:NM_018953:1428:165\t339\tNR_003084\t1572\t1\t50M\t=\t1457\t-165\tTATTTATTGACTCTGGGTCCTTCCTGAAACTATATTTTGTCATATCAAAT\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+8186:NM_018953:1442:153\t403\tNR_003084\t1574\t1\t50M\t=\t1471\t-153\tTTTATTGACTCTGGGTCCTTCCTGAAACTATATTTTGTCATATCAAATAA\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+3331:NM_018953:1404:193\t403\tNR_003084\t1576\t1\t50M\t=\t1433\t-193\tTATTGACTCTGGGTCCTTCCTGAAACTATATTTTGTCATATCAAATAAAG\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+2226:NM_018953:1422:177\t403\tNR_003084\t1578\t1\t50M\t=\t1451\t-177\tTTGACTCTGGGTCCTTCCTGAAACTATATTTTGTCATATCAAATAAAGAG\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+9853:NM_018953:1427:182\t403\tNR_003084\t1588\t1\t50M\t=\t1456\t-182\tGTCCTTCCTGAAACTATATTTTGTCATATCAAATAAAGAGAGAACAGGAC\t*\tNH:i:2\tHI:i:2\tAS:i:0\n"], "status": "failure"}}, {"id": "salmon/1.3.0+galaxy1-4", "has_data": true, "data": {"tool_id": "salmon", "tool_version": "1.3.0+galaxy1", "test_index": 4, "time_seconds": 26.383347272872925, "inputs": {"quant_type|refTranscriptSource|s_index|fasta": {"src": "hda", "id": "644b6371c0192d88"}, "quant_type|refTranscriptSource|TranscriptSource": "history", "quant_type|discardOrphansQuasi": false, "quant_type|validmap|validateMappings": true, "quant_type|dovetail": true, "quant_type|recoverOrphans": true, "quant_type|qtype": "reads"}, "job": {"model_class": "Job", "id": "765d4069e7f77bff", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:15:39.003440", "create_time": "2024-09-14T01:15:27.787287", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-wj2zq", "command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/a/0/a/dataset_a0a5a363-dd65-4ec5-ad4d-8114b0ac97ed.dat' && ln -s /galaxy/server/database/objects/a/0/a/dataset_a0a5a363-dd65-4ec5-ad4d-8114b0ac97ed.dat ./single.fasta && salmon quant --index './index' --libType U --unmatedReads ./single.fasta --threads \"${GALAXY_SLOTS:-4}\" --validateMappings --minScoreFraction '0.65' --ma '2' --mp '4' --go '5' --ge '3' --allowDovetail --recoverOrphans --incompatPrior '0.0' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '100' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '1e-05' -o ./output", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"biasSpeedSamp\": \"5\", \"bootstrapReproject\": false, \"dumpEq\": false, \"dumpEqWeights\": false, \"fldMax\": \"1000\", \"fldMean\": \"250\", \"fldSD\": \"25\", \"forgettingFactor\": \"0.65\", \"initUniform\": false, \"maxReadOcc\": \"100\", \"minAssignedFrags\": \"\", \"noBiasLengthThreshold\": false, \"noEffectiveLengthCorrection\": false, \"noFragLengthDist\": false, \"noGammaDraw\": false, \"noLengthCorrection\": false, \"numAuxModelSamples\": \"5000000\", \"numBiasSamples\": \"2000000\", \"numBootstraps\": \"0\", \"numGibbsSamples\": \"0\", \"numPreAuxModelSamples\": \"5000\", \"perTranscriptPrior\": false, \"rangeFactorizationBins\": \"0\", \"sigDigits\": \"3\", \"skipQuant\": false, \"thinningFactor\": \"16\", \"useEM\": false, \"vbPrior\": \"1e-05\", \"writeOrphanLinks\": false, \"writeUnmappedNames\": false}", "meta": "false", "incompatPrior": "\"0.0\"", "gcBias": "false", "seqBias": "false", "geneMap": null, "quant_type": "{\"__current_case__\": 0, \"consensusSlack\": \"0\", \"consistentHits\": false, \"discardOrphansQuasi\": false, \"dovetail\": true, \"input\": {\"single_or_paired\": {\"__current_case__\": 0, \"input_singles\": {\"values\": [{\"id\": 142, \"src\": \"hda\"}]}, \"single_or_paired_opts\": \"single\", \"strandedness\": \"U\"}}, \"qtype\": \"reads\", \"quasiCoverage\": \"\", \"recoverOrphans\": true, \"refTranscriptSource\": {\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 142, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}, \"type\": \"quasi\", \"validmap\": {\"__current_case__\": 0, \"gapExtensionPenalty\": \"3\", \"gapOpenPenalty\": \"5\", \"hardFilter\": false, \"matchScore\": \"2\", \"maxMMPExtension\": \"\", \"mimicBT2\": false, \"mimicStrictBT2\": false, \"minScoreFraction\": \"0.65\", \"mismatchPenalty\": \"4\", \"validateMappings\": true}, \"writeMappings\": false}"}, "inputs": {"quant_type|refTranscriptSource|s_index|fasta": {"id": "644b6371c0192d88", "src": "hda", "uuid": "a0a5a363-dd65-4ec5-ad4d-8114b0ac97ed"}, "quant_type|input|single_or_paired|input_singles": {"id": "644b6371c0192d88", "src": "hda", "uuid": "a0a5a363-dd65-4ec5-ad4d-8114b0ac97ed"}}, "outputs": {"output_quant": {"id": "13edf28a03b234a4", "src": "hda", "uuid": "62e35a26-421e-4fbb-a191-b44c2e9dcd92"}}, "output_collections": {}, "tool_stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 14\nFalse junctions count = 18\nHash table size = 32\nCandidate marks count = 56\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 51\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 14\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 105024 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "tool_stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n[2024-09-14 01:15:29.543] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-09-14 01:15:29.543] [jLog] [info] building index\nout : ./index\n[2024-09-14 01:15:29.544] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-09-14 01:15:29.552] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-09-14 01:15:29.552] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 15 cleaned references\n[2024-09-14 01:15:29.565] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-09-14 01:15:29.566] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20\nallowedIn: 12\nMax Junction ID: 70\nseen.size():569 kmerInfo.size():71\napproximateContigTotalLength: 17465\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 24 element count: 19592 complex nodes: 0\n# of ones in rank vector: 23\n[2024-09-14 01:15:29.625] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-09-14 01:15:29.625] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 19592\n-----------------------------------------\n| Loading contigs | Time = 1.2944 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading contig boundaries | Time = 718.91 us\n-----------------------------------------\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n23\n[2024-09-14 01:15:29.627] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-09-14 01:15:29.627] [puff::index::jointLog] [info] contig count for validation: 23\n[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] Total # of Contigs : 23\n[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] Total # of numerical Contigs : 23\n[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] Total # of contig vec entries: 36\n[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] bits per offset entry 6\n[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] Done constructing the contig vector. 24\n[2024-09-14 01:15:29.639] [puff::index::jointLog] [info] # segments = 23\n[2024-09-14 01:15:29.639] [puff::index::jointLog] [info] total length = 19592\n[2024-09-14 01:15:29.639] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] positional integer width = 15\n[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] seqSize = 19592\n[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] rankSize = 19592\n[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] num keys = 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elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-09-14 01:15:29.736] [puff::index::jointLog] [info] mphf size = 0.0125198 MB\n[2024-09-14 01:15:29.736] [puff::index::jointLog] [info] chunk size = 9796\n[2024-09-14 01:15:29.736] [puff::index::jointLog] [info] chunk 0 = [0, 9796)\n[2024-09-14 01:15:29.736] [puff::index::jointLog] [info] chunk 1 = [9796, 19562)\n[2024-09-14 01:15:29.737] [puff::index::jointLog] [info] finished populating pos vector\n[2024-09-14 01:15:29.737] [puff::index::jointLog] [info] writing index components\n[2024-09-14 01:15:29.751] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-09-14 01:15:29.757] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n### salmon (selective-alignment-based) v1.3.0\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { U }\n### [ unmatedReads ] => { ./single.fasta }\n### [ threads ] => { 6 }\n### [ validateMappings ] => { }\n### [ minScoreFraction ] => { 0.65 }\n### [ ma ] => { 2 }\n### [ mp ] => { 4 }\n### [ go ] => { 5 }\n### [ ge ] => { 3 }\n### [ allowDovetail ] => { }\n### [ recoverOrphans ] => { }\n### [ incompatPrior ] => { 0.0 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 100 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 1e-05 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n[2024-09-14 01:15:29.961] [jointLog] [info] setting maxHashResizeThreads to 6\n[2024-09-14 01:15:29.961] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-09-14 01:15:29.961] [jointLog] [warning] You set the mismatch penalty as 4, but it should be negative. It is being negated to -4.\n[2024-09-14 01:15:29.961] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.\n[2024-09-14 01:15:29.961] [jointLog] [info] parsing read library format\n[2024-09-14 01:15:29.961] [jointLog] [info] There is 1 library.\n-----------------------------------------\n| Loading contig table | Time = 1.1164 ms\n-----------------------------------------\nsize = 24\n-----------------------------------------\n| Loading contig offsets | Time = 2.1175 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 750.63 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 943.23 us\n-----------------------------------------\nsize = 19592\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 1.1738 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading sequence | Time = 1.2531 ms\n-----------------------------------------\n[2024-09-14 01:15:30.051] [jointLog] [info] Loading pufferfish index\n[2024-09-14 01:15:30.052] [jointLog] [info] Loading dense pufferfish index.\nsize = 18902\n-----------------------------------------\n| Loading positions | Time = 1.6923 ms\n-----------------------------------------\nsize = 28562\n-----------------------------------------\n| Loading reference sequence | Time = 848.79 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 571.89 us\n-----------------------------------------\n[2024-09-14 01:15:30.065] [jointLog] [info] done\n[2024-09-14 01:15:30.065] [jointLog] [info] Index contained 15 targets\n[2024-09-14 01:15:30.065] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2024-09-14 01:15:30.112] [jointLog] [info] Computed 15 rich equivalence classes for further processing\n[2024-09-14 01:15:30.112] [jointLog] [info] Counted 15 total reads in the equivalence classes \n[2024-09-14 01:15:30.114] [jointLog] [info] Number of orphans recovered using orphan rescue : 0\n[2024-09-14 01:15:30.114] [jointLog] [info] Number of mappings discarded because of alignment score : 6\n[2024-09-14 01:15:30.114] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2024-09-14 01:15:30.114] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-09-14 01:15:30.114] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2024-09-14 01:15:30.114] [jointLog] [info] Mapping rate = 100%\n\n[2024-09-14 01:15:30.114] [jointLog] [info] finished quantifyLibrary()\n[2024-09-14 01:15:30.118] [jointLog] [info] Starting optimizer\n[2024-09-14 01:15:30.119] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2024-09-14 01:15:30.119] [jointLog] [info] iteration = 0 | max rel diff. = 0\n[2024-09-14 01:15:30.120] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2024-09-14 01:15:30.120] [jointLog] [info] Finished optimizer\n[2024-09-14 01:15:30.120] [jointLog] [info] writing output \n\n[2024-09-14 01:15:30.125] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "job_stdout": "", "job_stderr": "", "stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n[2024-09-14 01:15:29.543] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-09-14 01:15:29.543] [jLog] [info] building index\nout : ./index\n[2024-09-14 01:15:29.544] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-09-14 01:15:29.552] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-09-14 01:15:29.552] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 15 cleaned references\n[2024-09-14 01:15:29.565] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-09-14 01:15:29.566] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20\nallowedIn: 12\nMax Junction ID: 70\nseen.size():569 kmerInfo.size():71\napproximateContigTotalLength: 17465\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 24 element count: 19592 complex nodes: 0\n# of ones in rank vector: 23\n[2024-09-14 01:15:29.625] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-09-14 01:15:29.625] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 19592\n-----------------------------------------\n| Loading contigs | Time = 1.2944 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading contig boundaries | Time = 718.91 us\n-----------------------------------------\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n23\n[2024-09-14 01:15:29.627] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-09-14 01:15:29.627] [puff::index::jointLog] [info] contig count for validation: 23\n[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] Total # of Contigs : 23\n[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] Total # of numerical Contigs : 23\n[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] Total # of contig vec entries: 36\n[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] bits per offset entry 6\n[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] Done constructing the contig vector. 24\n[2024-09-14 01:15:29.639] [puff::index::jointLog] [info] # segments = 23\n[2024-09-14 01:15:29.639] [puff::index::jointLog] [info] total length = 19592\n[2024-09-14 01:15:29.639] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] positional integer width = 15\n[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] seqSize = 19592\n[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] rankSize = 19592\n[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] num keys = 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elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-09-14 01:15:29.736] [puff::index::jointLog] [info] mphf size = 0.0125198 MB\n[2024-09-14 01:15:29.736] [puff::index::jointLog] [info] chunk size = 9796\n[2024-09-14 01:15:29.736] [puff::index::jointLog] [info] chunk 0 = [0, 9796)\n[2024-09-14 01:15:29.736] [puff::index::jointLog] [info] chunk 1 = [9796, 19562)\n[2024-09-14 01:15:29.737] [puff::index::jointLog] [info] finished populating pos vector\n[2024-09-14 01:15:29.737] [puff::index::jointLog] [info] writing index components\n[2024-09-14 01:15:29.751] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-09-14 01:15:29.757] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n### salmon (selective-alignment-based) v1.3.0\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { U }\n### [ unmatedReads ] => { ./single.fasta }\n### [ threads ] => { 6 }\n### [ validateMappings ] => { }\n### [ minScoreFraction ] => { 0.65 }\n### [ ma ] => { 2 }\n### [ mp ] => { 4 }\n### [ go ] => { 5 }\n### [ ge ] => { 3 }\n### [ allowDovetail ] => { }\n### [ recoverOrphans ] => { }\n### [ incompatPrior ] => { 0.0 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 100 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 1e-05 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n[2024-09-14 01:15:29.961] [jointLog] [info] setting maxHashResizeThreads to 6\n[2024-09-14 01:15:29.961] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-09-14 01:15:29.961] [jointLog] [warning] You set the mismatch penalty as 4, but it should be negative. It is being negated to -4.\n[2024-09-14 01:15:29.961] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.\n[2024-09-14 01:15:29.961] [jointLog] [info] parsing read library format\n[2024-09-14 01:15:29.961] [jointLog] [info] There is 1 library.\n-----------------------------------------\n| Loading contig table | Time = 1.1164 ms\n-----------------------------------------\nsize = 24\n-----------------------------------------\n| Loading contig offsets | Time = 2.1175 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 750.63 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 943.23 us\n-----------------------------------------\nsize = 19592\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 1.1738 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading sequence | Time = 1.2531 ms\n-----------------------------------------\n[2024-09-14 01:15:30.051] [jointLog] [info] Loading pufferfish index\n[2024-09-14 01:15:30.052] [jointLog] [info] Loading dense pufferfish index.\nsize = 18902\n-----------------------------------------\n| Loading positions | Time = 1.6923 ms\n-----------------------------------------\nsize = 28562\n-----------------------------------------\n| Loading reference sequence | Time = 848.79 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 571.89 us\n-----------------------------------------\n[2024-09-14 01:15:30.065] [jointLog] [info] done\n[2024-09-14 01:15:30.065] [jointLog] [info] Index contained 15 targets\n[2024-09-14 01:15:30.065] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2024-09-14 01:15:30.112] [jointLog] [info] Computed 15 rich equivalence classes for further processing\n[2024-09-14 01:15:30.112] [jointLog] [info] Counted 15 total reads in the equivalence classes \n[2024-09-14 01:15:30.114] [jointLog] [info] Number of orphans recovered using orphan rescue : 0\n[2024-09-14 01:15:30.114] [jointLog] [info] Number of mappings discarded because of alignment score : 6\n[2024-09-14 01:15:30.114] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2024-09-14 01:15:30.114] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-09-14 01:15:30.114] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2024-09-14 01:15:30.114] [jointLog] [info] Mapping rate = 100%\n\n[2024-09-14 01:15:30.114] [jointLog] [info] finished quantifyLibrary()\n[2024-09-14 01:15:30.118] [jointLog] [info] Starting optimizer\n[2024-09-14 01:15:30.119] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2024-09-14 01:15:30.119] [jointLog] [info] iteration = 0 | max rel diff. = 0\n[2024-09-14 01:15:30.120] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2024-09-14 01:15:30.120] [jointLog] [info] Finished optimizer\n[2024-09-14 01:15:30.120] [jointLog] [info] writing output \n\n[2024-09-14 01:15:30.125] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 14\nFalse junctions count = 18\nHash table size = 32\nCandidate marks count = 56\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 51\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 14\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 105024 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-14 01:15:30", "plugin": "core", "name": "end_epoch", "raw_value": "1726276530.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:15:29", "plugin": "core", "name": "start_epoch", "raw_value": "1726276529.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}]}, "status": "success"}}, {"id": "salmon/1.3.0+galaxy1-5", "has_data": true, "data": {"tool_id": "salmon", "tool_version": "1.3.0+galaxy1", "test_index": 5, "time_seconds": 27.314181566238403, "inputs": {"quant_type|refTranscriptSource|s_index|fasta": {"src": "hda", "id": "44693b64ca858b34"}, "quant_type|refTranscriptSource|TranscriptSource": "history", "quant_type|qtype": "reads", "seqBias": true, "gcBias": true, "adv|dumpEq": true, "adv|minAssignedFrags": "10", "adv|initUniform": true, "adv|noLengthCorrection": false, "adv|useEM": true, "adv|noGammaDraw": true}, "job": {"model_class": "Job", "id": "9a28a94cdc902f04", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:16:06.267378", "create_time": "2024-09-14T01:15:55.643143", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-9v7mh", "command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/1/b/f/dataset_1bfa5e66-2410-430c-b76b-ad0f89c622cf.dat' && ln -s /galaxy/server/database/objects/1/b/f/dataset_1bfa5e66-2410-430c-b76b-ad0f89c622cf.dat ./single.fasta && salmon quant --index './index' --libType U --unmatedReads ./single.fasta --threads \"${GALAXY_SLOTS:-4}\" --seqBias --gcBias --incompatPrior '0.0' --dumpEq --minAssignedFrags '10' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --initUniform --maxReadOcc '100' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --useEM --numGibbsSamples '0' --noGammaDraw --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '1e-05' -o ./output", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"biasSpeedSamp\": \"5\", \"bootstrapReproject\": false, \"dumpEq\": true, \"dumpEqWeights\": false, \"fldMax\": \"1000\", \"fldMean\": \"250\", \"fldSD\": \"25\", \"forgettingFactor\": \"0.65\", \"initUniform\": true, \"maxReadOcc\": \"100\", \"minAssignedFrags\": \"10\", \"noBiasLengthThreshold\": false, \"noEffectiveLengthCorrection\": false, \"noFragLengthDist\": false, \"noGammaDraw\": true, \"noLengthCorrection\": false, \"numAuxModelSamples\": \"5000000\", \"numBiasSamples\": \"2000000\", \"numBootstraps\": \"0\", \"numGibbsSamples\": \"0\", \"numPreAuxModelSamples\": \"5000\", \"perTranscriptPrior\": false, \"rangeFactorizationBins\": \"0\", \"sigDigits\": \"3\", \"skipQuant\": false, \"thinningFactor\": \"16\", \"useEM\": true, \"vbPrior\": \"1e-05\", \"writeOrphanLinks\": false, \"writeUnmappedNames\": false}", "meta": "false", "incompatPrior": "\"0.0\"", "gcBias": "true", "seqBias": "true", "geneMap": null, "quant_type": "{\"__current_case__\": 0, \"consensusSlack\": \"0\", \"consistentHits\": false, \"discardOrphansQuasi\": false, \"dovetail\": false, \"input\": {\"single_or_paired\": {\"__current_case__\": 0, \"input_singles\": {\"values\": [{\"id\": 144, \"src\": \"hda\"}]}, \"single_or_paired_opts\": \"single\", \"strandedness\": \"U\"}}, \"qtype\": \"reads\", \"quasiCoverage\": \"\", \"recoverOrphans\": false, \"refTranscriptSource\": {\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 144, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}, \"type\": \"quasi\", \"validmap\": {\"__current_case__\": 1, \"validateMappings\": false}, \"writeMappings\": false}"}, "inputs": {"quant_type|refTranscriptSource|s_index|fasta": {"id": "44693b64ca858b34", "src": "hda", "uuid": "1bfa5e66-2410-430c-b76b-ad0f89c622cf"}, "quant_type|input|single_or_paired|input_singles": {"id": "44693b64ca858b34", "src": "hda", "uuid": "1bfa5e66-2410-430c-b76b-ad0f89c622cf"}}, "outputs": {"output_quant": {"id": "8954f16e4bf094ce", "src": "hda", "uuid": "2ef95097-a72a-4d1f-9f2c-23c853c23b29"}}, "output_collections": {}, "tool_stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 14\nFalse junctions count = 18\nHash table size = 32\nCandidate marks count = 55\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 51\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 14\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 105024 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "tool_stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n[2024-09-14 01:15:57.355] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-09-14 01:15:57.355] [jLog] [info] building index\nout : ./index\n[2024-09-14 01:15:57.356] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-09-14 01:15:57.364] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-09-14 01:15:57.364] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 15 cleaned references\n[2024-09-14 01:15:57.377] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-09-14 01:15:57.378] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20\nallowedIn: 12\nMax Junction ID: 70\nseen.size():569 kmerInfo.size():71\napproximateContigTotalLength: 17465\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 24 element count: 19592 complex nodes: 0\n# of ones in rank vector: 23\n[2024-09-14 01:15:57.437] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-09-14 01:15:57.437] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 19592\n-----------------------------------------\n| Loading contigs | Time = 1.3213 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading contig boundaries | Time = 923.92 us\n-----------------------------------------\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n23\n[2024-09-14 01:15:57.440] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-09-14 01:15:57.440] [puff::index::jointLog] [info] contig count for validation: 23\n[2024-09-14 01:15:57.440] [puff::index::jointLog] [info] Total # of Contigs : 23\n[2024-09-14 01:15:57.440] [puff::index::jointLog] [info] Total # of numerical Contigs : 23\n[2024-09-14 01:15:57.441] [puff::index::jointLog] [info] Total # of contig vec entries: 36\n[2024-09-14 01:15:57.441] [puff::index::jointLog] [info] bits per offset entry 6\n[2024-09-14 01:15:57.441] [puff::index::jointLog] [info] Done constructing the contig vector. 24\n[2024-09-14 01:15:57.452] [puff::index::jointLog] [info] # segments = 23\n[2024-09-14 01:15:57.452] [puff::index::jointLog] [info] total length = 19592\n[2024-09-14 01:15:57.452] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-09-14 01:15:57.462] [puff::index::jointLog] [info] positional integer width = 15\n[2024-09-14 01:15:57.462] [puff::index::jointLog] [info] seqSize = 19592\n[2024-09-14 01:15:57.462] [puff::index::jointLog] [info] rankSize = 19592\n[2024-09-14 01:15:57.462] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-09-14 01:15:57.462] [puff::index::jointLog] [info] num keys = 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elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-09-14 01:15:57.548] [puff::index::jointLog] [info] mphf size = 0.0125198 MB\n[2024-09-14 01:15:57.548] [puff::index::jointLog] [info] chunk size = 9796\n[2024-09-14 01:15:57.548] [puff::index::jointLog] [info] chunk 0 = [0, 9796)\n[2024-09-14 01:15:57.548] [puff::index::jointLog] [info] chunk 1 = [9796, 19562)\n[2024-09-14 01:15:57.549] [puff::index::jointLog] [info] finished populating pos vector\n[2024-09-14 01:15:57.549] [puff::index::jointLog] [info] writing index components\n[2024-09-14 01:15:57.564] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-09-14 01:15:57.571] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n### salmon (selective-alignment-based) v1.3.0\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { U }\n### [ unmatedReads ] => { ./single.fasta }\n### [ threads ] => { 6 }\n### [ seqBias ] => { }\n### [ gcBias ] => { }\n### [ incompatPrior ] => { 0.0 }\n### [ dumpEq ] => { }\n### [ minAssignedFrags ] => { 10 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ initUniform ] => { }\n### [ maxReadOcc ] => { 100 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ useEM ] => { }\n### [ numGibbsSamples ] => { 0 }\n### [ noGammaDraw ] => { }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 1e-05 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n[2024-09-14 01:15:57.655] [jointLog] [info] setting maxHashResizeThreads to 6\n[2024-09-14 01:15:57.655] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-09-14 01:15:57.655] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-09-14 01:15:57.655] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.\n[2024-09-14 01:15:57.655] [jointLog] [info] parsing read library format\n[2024-09-14 01:15:57.655] [jointLog] [info] There is 1 library.\n-----------------------------------------\n| Loading contig table | Time = 750.35 us\n-----------------------------------------\nsize = 24\n-----------------------------------------\n| Loading contig offsets | Time = 1.2379 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 535.57 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 697.19 us\n-----------------------------------------\nsize = 19592\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 986.83 us\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading sequence | Time = 845.78 us\n-----------------------------------------\nsize = 18902\n-----------------------------------------\n| Loading positions | Time = 1.2133 ms\n-----------------------------------------\nsize = 28562\n-----------------------------------------\n| Loading reference sequence | Time = 404.68 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 368.4 us\n-----------------------------------------\n[2024-09-14 01:15:57.742] [jointLog] [info] Loading pufferfish index\n[2024-09-14 01:15:57.743] [jointLog] [info] Loading dense pufferfish index.\n[2024-09-14 01:15:57.752] [jointLog] [info] done\n[2024-09-14 01:15:57.752] [jointLog] [info] Index contained 15 targets\n[2024-09-14 01:15:57.753] [jointLog] [info] Number of decoys : 0\n[2024-09-14 01:15:57.753] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries. Please use this option with caution.\n\n\n\n\n\n\n\n\n\n\n\n\n[2024-09-14 01:15:57.800] [jointLog] [info] Computed 15 rich equivalence classes for further processing\n[2024-09-14 01:15:57.800] [jointLog] [info] Counted 15 total reads in the equivalence classes \n[2024-09-14 01:15:57.801] [jointLog] [info] Number of mappings discarded because of alignment score : 5\n[2024-09-14 01:15:57.801] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2024-09-14 01:15:57.801] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-09-14 01:15:57.801] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2024-09-14 01:15:57.801] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2024-09-14 01:15:57.801] [jointLog] [info] Mapping rate = 100%\n\n[2024-09-14 01:15:57.801] [jointLog] [info] finished quantifyLibrary()\n[2024-09-14 01:15:57.806] [jointLog] [info] Starting optimizer\n[2024-09-14 01:15:57.806] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2024-09-14 01:15:57.806] [jointLog] [info] iteration = 0 | max rel diff. = 49\n[2024-09-14 01:15:57.806] [jointLog] [info] iteration 3, adjusting effective lengths to account for biases\n[2024-09-14 01:15:57.811] [jointLog] [info] Computed expected counts (for bias correction)\n[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 20.0% of the transcripts\n[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 40.0% of the transcripts\n[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 46.7% of the transcripts\n[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 46.7% of the transcripts\n[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 46.7% of the transcripts\n[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 46.7% of the transcripts\n[2024-09-14 01:15:57.813] [jointLog] [info] processed bias for 53.3% of the transcripts\n[2024-09-14 01:15:57.813] [jointLog] [info] processed bias for 73.3% of the transcripts\n[2024-09-14 01:15:57.814] [jointLog] [info] processed bias for 100.0% of the transcripts\n[2024-09-14 01:15:57.814] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2024-09-14 01:15:57.814] [jointLog] [info] Finished optimizer\n[2024-09-14 01:15:57.814] [jointLog] [info] writing output \n\n[2024-09-14 01:15:57.819] [jointLog] [info] writing equivalence class counts.\n[2024-09-14 01:15:57.820] [jointLog] [info] Collapsing factorization information into simplified equivalence classes.\n[2024-09-14 01:15:57.820] [jointLog] [info] done.\n[2024-09-14 01:15:57.823] [jointLog] [info] done writing equivalence class counts.\n[2024-09-14 01:15:57.824] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "job_stdout": "", "job_stderr": "", "stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n[2024-09-14 01:15:57.355] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-09-14 01:15:57.355] [jLog] [info] building index\nout : ./index\n[2024-09-14 01:15:57.356] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-09-14 01:15:57.364] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-09-14 01:15:57.364] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 15 cleaned references\n[2024-09-14 01:15:57.377] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-09-14 01:15:57.378] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20\nallowedIn: 12\nMax Junction ID: 70\nseen.size():569 kmerInfo.size():71\napproximateContigTotalLength: 17465\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 24 element count: 19592 complex nodes: 0\n# of ones in rank vector: 23\n[2024-09-14 01:15:57.437] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-09-14 01:15:57.437] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 19592\n-----------------------------------------\n| Loading contigs | Time = 1.3213 ms\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading contig boundaries | Time = 923.92 us\n-----------------------------------------\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n23\n[2024-09-14 01:15:57.440] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-09-14 01:15:57.440] [puff::index::jointLog] [info] contig count for validation: 23\n[2024-09-14 01:15:57.440] [puff::index::jointLog] [info] Total # of Contigs : 23\n[2024-09-14 01:15:57.440] [puff::index::jointLog] [info] Total # of numerical Contigs : 23\n[2024-09-14 01:15:57.441] [puff::index::jointLog] [info] Total # of contig vec entries: 36\n[2024-09-14 01:15:57.441] [puff::index::jointLog] [info] bits per offset entry 6\n[2024-09-14 01:15:57.441] [puff::index::jointLog] [info] Done constructing the contig vector. 24\n[2024-09-14 01:15:57.452] [puff::index::jointLog] [info] # segments = 23\n[2024-09-14 01:15:57.452] [puff::index::jointLog] [info] total length = 19592\n[2024-09-14 01:15:57.452] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-09-14 01:15:57.462] [puff::index::jointLog] [info] positional integer width = 15\n[2024-09-14 01:15:57.462] [puff::index::jointLog] [info] seqSize = 19592\n[2024-09-14 01:15:57.462] [puff::index::jointLog] [info] rankSize = 19592\n[2024-09-14 01:15:57.462] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-09-14 01:15:57.462] [puff::index::jointLog] [info] num keys = 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min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-09-14 01:15:57.548] [puff::index::jointLog] [info] mphf size = 0.0125198 MB\n[2024-09-14 01:15:57.548] [puff::index::jointLog] [info] chunk size = 9796\n[2024-09-14 01:15:57.548] [puff::index::jointLog] [info] chunk 0 = [0, 9796)\n[2024-09-14 01:15:57.548] [puff::index::jointLog] [info] chunk 1 = [9796, 19562)\n[2024-09-14 01:15:57.549] [puff::index::jointLog] [info] finished populating pos vector\n[2024-09-14 01:15:57.549] [puff::index::jointLog] [info] writing index components\n[2024-09-14 01:15:57.564] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-09-14 01:15:57.571] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###\n### salmon (selective-alignment-based) v1.3.0\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { U }\n### [ unmatedReads ] => { ./single.fasta }\n### [ threads ] => { 6 }\n### [ seqBias ] => { }\n### [ gcBias ] => { }\n### [ incompatPrior ] => { 0.0 }\n### [ dumpEq ] => { }\n### [ minAssignedFrags ] => { 10 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ initUniform ] => { }\n### [ maxReadOcc ] => { 100 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ useEM ] => { }\n### [ numGibbsSamples ] => { 0 }\n### [ noGammaDraw ] => { }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 1e-05 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n[2024-09-14 01:15:57.655] [jointLog] [info] setting maxHashResizeThreads to 6\n[2024-09-14 01:15:57.655] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-09-14 01:15:57.655] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-09-14 01:15:57.655] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.\n[2024-09-14 01:15:57.655] [jointLog] [info] parsing read library format\n[2024-09-14 01:15:57.655] [jointLog] [info] There is 1 library.\n-----------------------------------------\n| Loading contig table | Time = 750.35 us\n-----------------------------------------\nsize = 24\n-----------------------------------------\n| Loading contig offsets | Time = 1.2379 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 535.57 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 697.19 us\n-----------------------------------------\nsize = 19592\nNumber of ones: 23\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 986.83 us\n-----------------------------------------\nsize = 19592\n-----------------------------------------\n| Loading sequence | Time = 845.78 us\n-----------------------------------------\nsize = 18902\n-----------------------------------------\n| Loading positions | Time = 1.2133 ms\n-----------------------------------------\nsize = 28562\n-----------------------------------------\n| Loading reference sequence | Time = 404.68 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 368.4 us\n-----------------------------------------\n[2024-09-14 01:15:57.742] [jointLog] [info] Loading pufferfish index\n[2024-09-14 01:15:57.743] [jointLog] [info] Loading dense pufferfish index.\n[2024-09-14 01:15:57.752] [jointLog] [info] done\n[2024-09-14 01:15:57.752] [jointLog] [info] Index contained 15 targets\n[2024-09-14 01:15:57.753] [jointLog] [info] Number of decoys : 0\n[2024-09-14 01:15:57.753] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries. Please use this option with caution.\n\n\n\n\n\n\n\n\n\n\n\n\n[2024-09-14 01:15:57.800] [jointLog] [info] Computed 15 rich equivalence classes for further processing\n[2024-09-14 01:15:57.800] [jointLog] [info] Counted 15 total reads in the equivalence classes \n[2024-09-14 01:15:57.801] [jointLog] [info] Number of mappings discarded because of alignment score : 5\n[2024-09-14 01:15:57.801] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2024-09-14 01:15:57.801] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-09-14 01:15:57.801] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2024-09-14 01:15:57.801] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2024-09-14 01:15:57.801] [jointLog] [info] Mapping rate = 100%\n\n[2024-09-14 01:15:57.801] [jointLog] [info] finished quantifyLibrary()\n[2024-09-14 01:15:57.806] [jointLog] [info] Starting optimizer\n[2024-09-14 01:15:57.806] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2024-09-14 01:15:57.806] [jointLog] [info] iteration = 0 | max rel diff. = 49\n[2024-09-14 01:15:57.806] [jointLog] [info] iteration 3, adjusting effective lengths to account for biases\n[2024-09-14 01:15:57.811] [jointLog] [info] Computed expected counts (for bias correction)\n[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 20.0% of the transcripts\n[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 40.0% of the transcripts\n[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 46.7% of the transcripts\n[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 46.7% of the transcripts\n[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 46.7% of the transcripts\n[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 46.7% of the transcripts\n[2024-09-14 01:15:57.813] [jointLog] [info] processed bias for 53.3% of the transcripts\n[2024-09-14 01:15:57.813] [jointLog] [info] processed bias for 73.3% of the transcripts\n[2024-09-14 01:15:57.814] [jointLog] [info] processed bias for 100.0% of the transcripts\n[2024-09-14 01:15:57.814] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2024-09-14 01:15:57.814] [jointLog] [info] Finished optimizer\n[2024-09-14 01:15:57.814] [jointLog] [info] writing output \n\n[2024-09-14 01:15:57.819] [jointLog] [info] writing equivalence class counts.\n[2024-09-14 01:15:57.820] [jointLog] [info] Collapsing factorization information into simplified equivalence classes.\n[2024-09-14 01:15:57.820] [jointLog] [info] done.\n[2024-09-14 01:15:57.823] [jointLog] [info] done writing equivalence class counts.\n[2024-09-14 01:15:57.824] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 14\nFalse junctions count = 18\nHash table size = 32\nCandidate marks count = 55\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 51\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 14\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 105024 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-14 01:15:58", "plugin": "core", "name": "end_epoch", "raw_value": "1726276558.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:15:57", "plugin": "core", "name": "start_epoch", "raw_value": "1726276557.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}]}, "status": "success"}}, {"id": "salmon/1.3.0+galaxy1-6", "has_data": true, "data": {"tool_id": "salmon", "tool_version": "1.3.0+galaxy1", "test_index": 6, "status": "skip"}}, {"id": "sam_to_bam/2.1.2-0", "has_data": true, "data": {"tool_id": "sam_to_bam", "tool_version": "2.1.2", "test_index": 0, "time_seconds": 8.827072143554688, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "sam_to_bam/2.1.2-1", "has_data": true, "data": {"tool_id": "sam_to_bam", "tool_version": "2.1.2", "test_index": 1, "status": "skip"}}, {"id": "sam_to_bam/2.1.2-2", "has_data": true, "data": {"tool_id": "sam_to_bam", "tool_version": "2.1.2", "test_index": 2, "time_seconds": 33.405641078948975, "inputs": {"input": {"src": "hda", "id": "c12cff306b1f27cd"}, "addref_cond|ref": {"src": "hda", "id": "2611c7230f4ebe6d"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "95a0a0882149fa40", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:01:15.342757", "create_time": "2024-09-14T01:00:58.895654", "galaxy_version": "23.1", "command_version": "Version: 1.20 (using htslib 1.20)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2", "history_id": "ed165837e8ba4cca", "external_id": "gxy-btzww", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && reffa=\"reference.fa\" && ln -s '/galaxy/server/database/objects/4/1/c/dataset_41c32e09-608f-4ddf-85e2-13bea3229eb4.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools view -b -@ $addthreads -t \"$reffai\" '/galaxy/server/database/objects/4/c/3/dataset_4c33dcfc-06db-4200-9078-534cadb9f3e5.dat' | samtools sort -O bam -@ $addthreads -m $addmemory\"M\" -o '/galaxy/server/database/objects/e/4/3/dataset_e431d350-d031-4393-a6b3-5df0c270103b.dat' -T \"${TMPDIR:-.}\"", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"equCab2\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/equCab2.len\"", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 74, \"src\": \"hda\"}]}}"}, "inputs": {"addref_cond|ref": {"id": "2611c7230f4ebe6d", "src": "hda", "uuid": "41c32e09-608f-4ddf-85e2-13bea3229eb4"}, "input": {"id": "c12cff306b1f27cd", "src": "hda", "uuid": "4c33dcfc-06db-4200-9078-534cadb9f3e5"}}, "outputs": {"output1": {"id": "dc1abf31b7878b39", "src": "hda", "uuid": "e431d350-d031-4393-a6b3-5df0c270103b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-14 01:01:06", "plugin": "core", "name": "end_epoch", "raw_value": "1726275666.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:01:06", "plugin": "core", "name": "start_epoch", "raw_value": "1726275666.0000000"}, {"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_to_bam/2.1.2-3", "has_data": true, "data": {"tool_id": "sam_to_bam", "tool_version": "2.1.2", "test_index": 3, "time_seconds": 27.55599308013916, "inputs": {"input": {"src": "hda", "id": "b355a78f591d3088"}, "addref_cond|ref": {"src": "hda", "id": "b94e2d0d46c75809"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "1762d3613701af86", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:01:43.176875", "create_time": "2024-09-14T01:01:32.893294", "galaxy_version": "23.1", "command_version": "Version: 1.20 (using htslib 1.20)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.2", "history_id": "ed165837e8ba4cca", "external_id": "gxy-dgjx4", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && reffa=\"reference.fa.gz\" && ln -s '/galaxy/server/database/objects/b/2/c/dataset_b2ce373b-8a50-4fdb-b724-cbaadfe6aad6.dat' $reffa && { samtools faidx $reffa || { echo \"Failed to index compressed reference. 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"2024-09-14T00:59:56.359901", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9", "history_id": "ed165837e8ba4cca", "external_id": "gxy-kn6bv", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -n -O BAM -o namesorted.bam '/galaxy/server/database/objects/8/6/a/dataset_86af6636-b6a5-414c-abe9-d126745b097d.dat' && samtools fixmate -@ $addthreads -c -O BAM namesorted.bam '/galaxy/server/database/objects/b/d/0/dataset_bd0e801d-4044-4546-8ed4-0b3a50ed5ea8.dat'", "traceback": null, "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addms": "false", "tempcigar": "true", "noprop": "false", "remsec": "false"}, "inputs": {"bamfile": {"id": "1a9d1a58818c88c1", "src": "hda", "uuid": "86af6636-b6a5-414c-abe9-d126745b097d"}}, "outputs": {"output": {"id": "ab33a4ba552f72dc", "src": "hda", "uuid": "bd0e801d-4044-4546-8ed4-0b3a50ed5ea8"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-14 00:59:58", "plugin": "core", "name": "end_epoch", "raw_value": "1726275598.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 00:59:58", "plugin": "core", "name": "start_epoch", "raw_value": "1726275598.0000000"}, {"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_fixmate/1.9-5", "has_data": true, "data": {"tool_id": "samtools_fixmate", "tool_version": "1.9", "test_index": 5, "time_seconds": 25.154863834381104, "inputs": {"bamfile": {"src": "hda", "id": "87dadb2c71819a0b"}}, "job": {"model_class": "Job", "id": "4fe3ac1409aa61b5", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:00:31.820285", "create_time": "2024-09-14T01:00:22.137554", "galaxy_version": "23.1", "command_version": "Version: 1.9 (using htslib 1.9)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.9", "history_id": "ed165837e8ba4cca", "external_id": "gxy-n7tx9", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -n -O BAM -o namesorted.bam '/galaxy/server/database/objects/a/c/c/dataset_acc0c902-0bf8-48c1-8798-2700ee364ab7.dat' && samtools fixmate -@ $addthreads -O BAM namesorted.bam '/galaxy/server/database/objects/f/5/9/dataset_f59012cb-1c29-4dbd-b749-baeaba5e6402.dat'", "traceback": null, "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addms": "false", "tempcigar": "false", "noprop": "false", "remsec": "false"}, "inputs": {"bamfile": {"id": "87dadb2c71819a0b", "src": "hda", "uuid": "acc0c902-0bf8-48c1-8798-2700ee364ab7"}}, "outputs": {"output": {"id": "4b3b265db2b6345e", "src": "hda", "uuid": "f59012cb-1c29-4dbd-b749-baeaba5e6402"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-14 01:00:23", "plugin": "core", "name": "end_epoch", "raw_value": "1726275623.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:00:23", "plugin": "core", "name": "start_epoch", "raw_value": "1726275623.0000000"}, {"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": "trimmomatic/0.38.1-0", "has_data": true, "data": {"tool_id": "trimmomatic", "tool_version": "0.38.1", "test_index": 0, "time_seconds": 43.027053117752075, "inputs": {"readtype|fastq_in": {"src": "hda", "id": "a57289ad4f175228"}, "readtype|single_or_paired": "se", "operations_0|operation|name": "SLIDINGWINDOW", "output_logs": true, "output_err": true}, "job": {"model_class": "Job", "id": "a57289ad4f175228", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T00:53:10.791471", "create_time": "2024-09-14T00:52:45.455453", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-jdmmb", "command_line": "if [ -z \"$TRIMMOMATIC_JAR_PATH\" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z \"$TRIMMOMATIC_ADAPTERS_PATH\" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/7/3/e/dataset_73eedd44-ddbb-4f2d-8dde-5dfd5a60c948.dat' fastq_in.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger' fastq_out.'fastqsanger' SLIDINGWINDOW:4:20 -trimlog trimlog 2>&1 | tee trimmomatic.log && if [ -z \"$(tail -1 trimmomatic.log | grep \"Completed successfully\")\" ]; then echo \"Trimmomatic did not finish successfully\" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger' '/galaxy/server/database/objects/3/5/a/dataset_35ab1889-5e9b-4f85-984d-7ac85d5d87af.dat'", "traceback": null, "params": {"readtype": "{\"__current_case__\": 0, \"fastq_in\": {\"values\": [{\"id\": 12, \"src\": \"hda\"}]}, \"single_or_paired\": \"se\"}", "illuminaclip": "{\"__current_case__\": 1, \"do_illuminaclip\": false}", "operations": "[{\"__index__\": 0, \"operation\": {\"__current_case__\": 0, \"name\": \"SLIDINGWINDOW\", \"required_quality\": \"20\", \"window_size\": \"4\"}}]", "output_logs": "true", "output_err": "true", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastqsanger\""}, "inputs": {"readtype|fastq_in": {"id": "a57289ad4f175228", "src": "hda", "uuid": "73eedd44-ddbb-4f2d-8dde-5dfd5a60c948"}}, "outputs": {"fastq_out": {"id": "fe0a9ea15b54bf6c", "src": "hda", "uuid": "35ab1889-5e9b-4f85-984d-7ac85d5d87af"}, "log_file": {"id": "defb5211a6a94aa8", "src": "hda", "uuid": "cf220079-4323-49eb-9ac7-0a9883096b20"}, "err_file": {"id": "0c8c289d788b4c08", "src": "hda", "uuid": "aa92a19e-03d0-4938-a23c-88c25d7ae205"}}, "output_collections": {}, "tool_stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticSE: Started with arguments:\n -threads 6 fastq_in.fastqsanger fastq_out.fastqsanger SLIDINGWINDOW:4:20 -trimlog trimlog\nQuality encoding detected as phred33\nInput Reads: 10 Surviving: 8 (80.00%) Dropped: 2 (20.00%)\nTrimmomaticSE: Completed successfully\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticSE: Started with arguments:\n -threads 6 fastq_in.fastqsanger fastq_out.fastqsanger SLIDINGWINDOW:4:20 -trimlog trimlog\nQuality encoding detected as phred33\nInput Reads: 10 Surviving: 8 (80.00%) Dropped: 2 (20.00%)\nTrimmomaticSE: Completed successfully\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-14 00:52:59", "plugin": "core", "name": "end_epoch", "raw_value": "1726275179.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 00:52:59", "plugin": "core", "name": "start_epoch", "raw_value": "1726275179.0000000"}, {"title": "Memory Allocated (MB)", "value": "12884", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12884.0000000"}, {"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}]}, "output_problems": ["Output err_file: different than expected, difference (using diff):\n( /tmp/tmpxlm10om0trimmomatic_se_out1.err v. /tmp/tmpse9d3e9jtrimmomatic_se_out1.err )\n--- local_file\n+++ history_data\n@@ -1,5 +1,6 @@\n+Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\n TrimmomaticSE: Started with arguments:\n- -threads 1 fastq_in.fastqsanger fastq_out.fastqsanger SLIDINGWINDOW:4:20 -trimlog trimlog\n+ -threads 6 fastq_in.fastqsanger fastq_out.fastqsanger SLIDINGWINDOW:4:20 -trimlog trimlog\n Quality encoding detected as phred33\n Input Reads: 10 Surviving: 8 (80.00%) Dropped: 2 (20.00%)\n TrimmomaticSE: Completed successfully\n"], "status": "failure"}}, {"id": "trimmomatic/0.38.1-1", "has_data": true, "data": {"tool_id": "trimmomatic", "tool_version": "0.38.1", "test_index": 1, "time_seconds": 9.834558010101318, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "trimmomatic/0.38.1-10", "has_data": true, "data": {"tool_id": "trimmomatic", "tool_version": "0.38.1", "test_index": 10, "time_seconds": 19.35331630706787, "inputs": {"readtype|fastq_in": {"src": "hda", "id": "346ee1d2fcf7f70c"}, "readtype|single_or_paired": "se", "operations_0|operation|target_length": "75", "operations_0|operation|strictness": "0.8", "operations_0|operation|name": "MAXINFO"}, "job": {"model_class": "Job", "id": "da2d40552de3029b", "state": "error", "exit_code": null, "update_time": "2024-09-14T00:56:52.038033", "create_time": "2024-09-14T00:56:47.840310", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-q74tk", "command_line": "if [ -z \"$TRIMMOMATIC_JAR_PATH\" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z \"$TRIMMOMATIC_ADAPTERS_PATH\" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/3/7/7/dataset_37778b71-9669-4df5-880b-532f8c4b276b.dat' fastq_in.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger' fastq_out.'fastqsanger' MAXINFO:75:0.8 2>&1 | tee trimmomatic.log && if [ -z \"$(tail -1 trimmomatic.log | grep \"Completed successfully\")\" ]; then echo \"Trimmomatic did not finish successfully\" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger' '/galaxy/server/database/objects/e/6/a/dataset_e6ac6186-9f77-45ca-a14f-43c8894a7811.dat'", "traceback": null, "params": {"__input_ext": "\"fastqsanger\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_err": "false", "output_logs": "false", "operations": "[{\"__index__\": 0, \"operation\": {\"__current_case__\": 7, \"name\": \"MAXINFO\", \"strictness\": \"0.8\", \"target_length\": \"75\"}}]", "illuminaclip": "{\"__current_case__\": 1, \"do_illuminaclip\": false}", "readtype": "{\"__current_case__\": 0, \"fastq_in\": {\"values\": [{\"id\": 45, \"src\": \"hda\"}]}, \"single_or_paired\": \"se\"}"}, "inputs": {"readtype|fastq_in": {"id": "346ee1d2fcf7f70c", "src": "hda", "uuid": "37778b71-9669-4df5-880b-532f8c4b276b"}}, "outputs": {"fastq_out": {"id": "50872bd7722d341d", "src": "hda", "uuid": "e6ac6186-9f77-45ca-a14f-43c8894a7811"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stderr": "", "stdout": "", "job_messages": null, "dependencies": [], "user_email": "tests@fake.org", "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "trimmomatic/0.38.1-11", "has_data": true, "data": {"tool_id": "trimmomatic", "tool_version": "0.38.1", "test_index": 11, "time_seconds": 29.056652784347534, "inputs": {"readtype|fastq_r1_in": {"src": "hda", "id": "9907fa81e6c94704"}, "readtype|fastq_r2_in": {"src": "hda", "id": "169d16a8c5164f68"}, "readtype|single_or_paired": "pair_of_files", "illuminaclip|adapter_type|adapter_fasta": "TruSeq2-PE.fa", "illuminaclip|do_illuminaclip": true, "operations_0|operation|name": "SLIDINGWINDOW"}, "job": {"model_class": "Job", "id": "3e0e92ef37a541d1", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T00:57:18.561482", "create_time": "2024-09-14T00:57:08.058731", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-zvbkb", "command_line": "if [ -z \"$TRIMMOMATIC_JAR_PATH\" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z \"$TRIMMOMATIC_ADAPTERS_PATH\" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/b/7/4/dataset_b74d1d24-cc83-446c-8e1b-fb992fd7d3d0.dat' fastq_r1.'fastqsanger' && ln -s '/galaxy/server/database/objects/b/b/a/dataset_bba28ac0-b3cc-4554-aad7-1a22ba1bf5f1.dat' fastq_r2.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar PE -threads ${GALAXY_SLOTS:-6} fastq_r1.'fastqsanger' fastq_r2.'fastqsanger' fastq_out_r1_paired.'fastqsanger' fastq_out_r1_unpaired.'fastqsanger' fastq_out_r2_paired.'fastqsanger' fastq_out_r2_unpaired.'fastqsanger' ILLUMINACLIP:$TRIMMOMATIC_ADAPTERS_PATH/TruSeq2-PE.fa:2:30:10:8:true SLIDINGWINDOW:4:20 2>&1 | tee trimmomatic.log && if [ -z \"$(tail -1 trimmomatic.log | grep \"Completed successfully\")\" ]; then echo \"Trimmomatic did not finish successfully\" >&2 ; exit 1 ; fi && mv fastq_out_r1_paired.'fastqsanger' '/galaxy/server/database/objects/e/b/e/dataset_ebefc30b-64a9-4eaa-8ad4-90b220b8f810.dat' && mv fastq_out_r1_unpaired.'fastqsanger' '/galaxy/server/database/objects/2/e/d/dataset_2ed584e0-3edb-42f1-98d7-76aefc7d8ce4.dat' && mv fastq_out_r2_paired.'fastqsanger' '/galaxy/server/database/objects/2/b/1/dataset_2b19ddb7-e787-4a65-83db-984b32389de8.dat' && mv fastq_out_r2_unpaired.'fastqsanger' '/galaxy/server/database/objects/3/4/7/dataset_34763ef0-a6f1-4296-a0fd-a1380ef45a17.dat'", "traceback": null, "params": {"__input_ext": "\"fastqsanger\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_err": "false", "output_logs": "false", "operations": "[{\"__index__\": 0, \"operation\": {\"__current_case__\": 0, \"name\": \"SLIDINGWINDOW\", \"required_quality\": \"20\", \"window_size\": \"4\"}}]", "illuminaclip": "{\"__current_case__\": 0, \"adapter_type\": {\"__current_case__\": 0, \"adapter_fasta\": \"TruSeq2-PE.fa\", \"standard_or_custom\": \"standard\"}, \"do_illuminaclip\": true, \"keep_both_reads\": true, \"min_adapter_len\": \"8\", \"palindrome_clip_threshold\": \"30\", \"seed_mismatches\": \"2\", \"simple_clip_threshold\": \"10\"}", "readtype": "{\"__current_case__\": 1, \"fastq_r1_in\": {\"values\": [{\"id\": 47, \"src\": \"hda\"}]}, \"fastq_r2_in\": {\"values\": [{\"id\": 48, \"src\": \"hda\"}]}, \"single_or_paired\": \"pair_of_files\"}"}, "inputs": {"readtype|fastq_r1_in": {"id": "9907fa81e6c94704", "src": "hda", "uuid": "b74d1d24-cc83-446c-8e1b-fb992fd7d3d0"}, "readtype|fastq_r2_in": {"id": "169d16a8c5164f68", "src": "hda", "uuid": "bba28ac0-b3cc-4554-aad7-1a22ba1bf5f1"}}, "outputs": {"fastq_out_r1_paired": {"id": "9184366d0e5e1098", "src": "hda", "uuid": "ebefc30b-64a9-4eaa-8ad4-90b220b8f810"}, "fastq_out_r2_paired": {"id": "517cff8f48d5d3c0", "src": "hda", "uuid": "2b19ddb7-e787-4a65-83db-984b32389de8"}, "fastq_out_r1_unpaired": {"id": "d0d1c4024af98dfb", "src": "hda", "uuid": "2ed584e0-3edb-42f1-98d7-76aefc7d8ce4"}, "fastq_out_r2_unpaired": {"id": "4fe3ac1409aa61b5", "src": "hda", "uuid": "34763ef0-a6f1-4296-a0fd-a1380ef45a17"}}, "output_collections": {}, "tool_stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticPE: Started with arguments:\n -threads 6 fastq_r1.fastqsanger fastq_r2.fastqsanger fastq_out_r1_paired.fastqsanger fastq_out_r1_unpaired.fastqsanger fastq_out_r2_paired.fastqsanger fastq_out_r2_unpaired.fastqsanger ILLUMINACLIP:/usr/local/share/trimmomatic-0.38-1/adapters/TruSeq2-PE.fa:2:30:10:8:true SLIDINGWINDOW:4:20\nUsing PrefixPair: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'\nUsing Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'\nUsing Long Clipping Sequence: 'AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG'\nUsing Long Clipping Sequence: 'TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC'\nUsing Long Clipping Sequence: 'TTTTTTTTTTCAAGCAGAAGACGGCATACGA'\nUsing Long Clipping Sequence: 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'\nUsing Long Clipping Sequence: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT'\nILLUMINACLIP: Using 1 prefix pairs, 6 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\nQuality encoding detected as phred33\nInput Read Pairs: 10 Both Surviving: 8 (80.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 2 (20.00%) Dropped: 0 (0.00%)\nTrimmomaticPE: Completed successfully\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticPE: Started with arguments:\n -threads 6 fastq_r1.fastqsanger fastq_r2.fastqsanger fastq_out_r1_paired.fastqsanger fastq_out_r1_unpaired.fastqsanger fastq_out_r2_paired.fastqsanger fastq_out_r2_unpaired.fastqsanger ILLUMINACLIP:/usr/local/share/trimmomatic-0.38-1/adapters/TruSeq2-PE.fa:2:30:10:8:true SLIDINGWINDOW:4:20\nUsing PrefixPair: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'\nUsing Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'\nUsing Long Clipping Sequence: 'AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG'\nUsing Long Clipping Sequence: 'TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC'\nUsing Long Clipping Sequence: 'TTTTTTTTTTCAAGCAGAAGACGGCATACGA'\nUsing Long Clipping Sequence: 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'\nUsing Long Clipping Sequence: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT'\nILLUMINACLIP: Using 1 prefix pairs, 6 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\nQuality encoding detected as phred33\nInput Read Pairs: 10 Both Surviving: 8 (80.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 2 (20.00%) Dropped: 0 (0.00%)\nTrimmomaticPE: Completed successfully\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}, {"title": "Memory Allocated (MB)", "value": "12884", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12884.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 00:57:09", "plugin": "core", "name": "start_epoch", "raw_value": "1726275429.0000000"}, {"title": "Job End Time", "value": "2024-09-14 00:57:10", "plugin": "core", "name": "end_epoch", "raw_value": "1726275430.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "trimmomatic/0.38.1-12", "has_data": true, "data": {"tool_id": "trimmomatic", "tool_version": "0.38.1", "test_index": 12, "time_seconds": 28.82190227508545, "inputs": {"readtype|fastq_r1_in": {"src": "hda", "id": "0aec0cc69095fb2b"}, "readtype|fastq_r2_in": {"src": "hda", "id": "219eea5edfdc4ae8"}, "readtype|single_or_paired": "pair_of_files", "illuminaclip|adapter_type|adapter_text": ">PrefixPE/1\nAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n>PrefixPE/2\nCAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\n>PCR_Primer1\nAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n>PCR_Primer1_rc\nAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT\n>PCR_Primer2\nCAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\n>PCR_Primer2_rc\nAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG\n>FlowCell1\nTTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC\n>FlowCell2\nTTTTTTTTTTCAAGCAGAAGACGGCATACGA\n", "illuminaclip|adapter_type|standard_or_custom": "custom", "illuminaclip|do_illuminaclip": true, "operations_0|operation|name": "SLIDINGWINDOW"}, "job": {"model_class": "Job", "id": "873462c21322a5f4", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T00:57:47.318063", "create_time": "2024-09-14T00:57:37.400528", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-wrh74", "command_line": "if [ -z \"$TRIMMOMATIC_JAR_PATH\" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z \"$TRIMMOMATIC_ADAPTERS_PATH\" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/b/a/c/dataset_bacff905-1aea-4550-8e00-06b2da9d0d44.dat' fastq_r1.'fastqsanger' && ln -s '/galaxy/server/database/objects/7/c/4/dataset_7c4914e7-e63d-4a57-ba43-c56a3c9e5b9e.dat' fastq_r2.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar PE -threads ${GALAXY_SLOTS:-6} fastq_r1.'fastqsanger' fastq_r2.'fastqsanger' fastq_out_r1_paired.'fastqsanger' fastq_out_r1_unpaired.'fastqsanger' fastq_out_r2_paired.'fastqsanger' fastq_out_r2_unpaired.'fastqsanger' ILLUMINACLIP:/galaxy/server/database/jobs_directory/000/40/configs/tmpt_pbf1wi:2:30:10:8:true SLIDINGWINDOW:4:20 2>&1 | tee trimmomatic.log && if [ -z \"$(tail -1 trimmomatic.log | grep \"Completed successfully\")\" ]; then echo \"Trimmomatic did not finish successfully\" >&2 ; exit 1 ; fi && mv fastq_out_r1_paired.'fastqsanger' '/galaxy/server/database/objects/6/8/d/dataset_68d481dc-c54b-4615-9c9d-b2fbf44c03e1.dat' && mv fastq_out_r1_unpaired.'fastqsanger' '/galaxy/server/database/objects/b/a/6/dataset_ba65a7a6-dd02-4d71-a498-457c47b73d4c.dat' && mv fastq_out_r2_paired.'fastqsanger' '/galaxy/server/database/objects/e/a/2/dataset_ea23499c-9ddf-4ab5-b3af-d7aca44fca60.dat' && mv fastq_out_r2_unpaired.'fastqsanger' '/galaxy/server/database/objects/c/e/0/dataset_ce021ec2-5f0a-4305-92d1-88a7fb78e9c4.dat'", "traceback": null, "params": {"__input_ext": "\"fastqsanger\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_err": "false", "output_logs": "false", "operations": "[{\"__index__\": 0, \"operation\": {\"__current_case__\": 0, \"name\": \"SLIDINGWINDOW\", \"required_quality\": \"20\", \"window_size\": \"4\"}}]", "illuminaclip": "{\"__current_case__\": 0, \"adapter_type\": {\"__current_case__\": 1, \"adapter_text\": \">PrefixPE/1\\nAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\\n>PrefixPE/2\\nCAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\\n>PCR_Primer1\\nAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\\n>PCR_Primer1_rc\\nAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT\\n>PCR_Primer2\\nCAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\\n>PCR_Primer2_rc\\nAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG\\n>FlowCell1\\nTTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC\\n>FlowCell2\\nTTTTTTTTTTCAAGCAGAAGACGGCATACGA\\n\", \"standard_or_custom\": \"custom\"}, \"do_illuminaclip\": true, \"keep_both_reads\": true, \"min_adapter_len\": \"8\", \"palindrome_clip_threshold\": \"30\", \"seed_mismatches\": \"2\", \"simple_clip_threshold\": \"10\"}", "readtype": "{\"__current_case__\": 1, \"fastq_r1_in\": {\"values\": [{\"id\": 53, \"src\": \"hda\"}]}, \"fastq_r2_in\": {\"values\": [{\"id\": 54, \"src\": \"hda\"}]}, \"single_or_paired\": \"pair_of_files\"}"}, "inputs": {"readtype|fastq_r1_in": {"id": "0aec0cc69095fb2b", "src": "hda", "uuid": "bacff905-1aea-4550-8e00-06b2da9d0d44"}, "readtype|fastq_r2_in": {"id": "219eea5edfdc4ae8", "src": "hda", "uuid": "7c4914e7-e63d-4a57-ba43-c56a3c9e5b9e"}}, "outputs": {"fastq_out_r1_paired": {"id": "5df7adb272208d2d", "src": "hda", "uuid": "68d481dc-c54b-4615-9c9d-b2fbf44c03e1"}, "fastq_out_r2_paired": {"id": "2ea84bc3d4af7b79", "src": "hda", "uuid": "ea23499c-9ddf-4ab5-b3af-d7aca44fca60"}, "fastq_out_r1_unpaired": {"id": "95a0a0882149fa40", "src": "hda", "uuid": "ba65a7a6-dd02-4d71-a498-457c47b73d4c"}, "fastq_out_r2_unpaired": {"id": "58bcb7304f57378f", "src": "hda", "uuid": "ce021ec2-5f0a-4305-92d1-88a7fb78e9c4"}}, "output_collections": {}, "tool_stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticPE: Started with arguments:\n -threads 6 fastq_r1.fastqsanger fastq_r2.fastqsanger fastq_out_r1_paired.fastqsanger fastq_out_r1_unpaired.fastqsanger fastq_out_r2_paired.fastqsanger fastq_out_r2_unpaired.fastqsanger ILLUMINACLIP:/galaxy/server/database/jobs_directory/000/40/configs/tmpt_pbf1wi:2:30:10:8:true SLIDINGWINDOW:4:20\nUsing PrefixPair: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'\nUsing Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'\nUsing Long Clipping Sequence: 'AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG'\nUsing Long Clipping Sequence: 'TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC'\nUsing Long Clipping Sequence: 'TTTTTTTTTTCAAGCAGAAGACGGCATACGA'\nUsing Long Clipping Sequence: 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'\nUsing Long Clipping Sequence: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT'\nILLUMINACLIP: Using 1 prefix pairs, 6 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\nQuality encoding detected as phred33\nInput Read Pairs: 10 Both Surviving: 8 (80.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 2 (20.00%) Dropped: 0 (0.00%)\nTrimmomaticPE: Completed successfully\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticPE: Started with arguments:\n -threads 6 fastq_r1.fastqsanger fastq_r2.fastqsanger fastq_out_r1_paired.fastqsanger fastq_out_r1_unpaired.fastqsanger fastq_out_r2_paired.fastqsanger fastq_out_r2_unpaired.fastqsanger ILLUMINACLIP:/galaxy/server/database/jobs_directory/000/40/configs/tmpt_pbf1wi:2:30:10:8:true SLIDINGWINDOW:4:20\nUsing PrefixPair: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'\nUsing Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'\nUsing Long Clipping Sequence: 'AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG'\nUsing Long Clipping Sequence: 'TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC'\nUsing Long Clipping Sequence: 'TTTTTTTTTTCAAGCAGAAGACGGCATACGA'\nUsing Long Clipping Sequence: 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'\nUsing Long Clipping Sequence: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT'\nILLUMINACLIP: Using 1 prefix pairs, 6 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\nQuality encoding detected as phred33\nInput Read Pairs: 10 Both Surviving: 8 (80.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 2 (20.00%) Dropped: 0 (0.00%)\nTrimmomaticPE: Completed successfully\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}, {"title": "Memory Allocated (MB)", "value": "12884", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12884.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 00:57:38", "plugin": "core", "name": "start_epoch", "raw_value": "1726275458.0000000"}, {"title": "Job End Time", "value": "2024-09-14 00:57:38", "plugin": "core", "name": "end_epoch", "raw_value": "1726275458.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "trimmomatic/0.38.1-2", "has_data": true, "data": {"tool_id": "trimmomatic", "tool_version": "0.38.1", "test_index": 2, "time_seconds": 30.340423583984375, "inputs": {"readtype|fastq_r1_in": {"src": "hda", "id": "c0c8a69c8070f677"}, "readtype|fastq_r2_in": {"src": "hda", "id": "4a12ddb120e74961"}, "readtype|single_or_paired": "pair_of_files", "operations_0|operation|name": "SLIDINGWINDOW"}, "job": {"model_class": "Job", "id": "7bf7e48be40dc04d", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T00:53:50.215090", "create_time": "2024-09-14T00:53:39.315666", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-f6x22", "command_line": "if [ -z \"$TRIMMOMATIC_JAR_PATH\" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z \"$TRIMMOMATIC_ADAPTERS_PATH\" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/5/3/5/dataset_53530603-4b11-4771-b00f-55b679cdffef.dat' fastq_r1.'fastqsanger.gz' && ln -s '/galaxy/server/database/objects/3/7/6/dataset_376767a6-2c00-4bc6-9292-29286bacc97d.dat' fastq_r2.'fastqsanger.gz' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar PE -threads ${GALAXY_SLOTS:-6} fastq_r1.'fastqsanger.gz' fastq_r2.'fastqsanger.gz' fastq_out_r1_paired.'fastqsanger.gz' fastq_out_r1_unpaired.'fastqsanger.gz' fastq_out_r2_paired.'fastqsanger.gz' fastq_out_r2_unpaired.'fastqsanger.gz' SLIDINGWINDOW:4:20 2>&1 | tee trimmomatic.log && if [ -z \"$(tail -1 trimmomatic.log | grep \"Completed successfully\")\" ]; then echo \"Trimmomatic did not finish successfully\" >&2 ; exit 1 ; fi && mv fastq_out_r1_paired.'fastqsanger.gz' '/galaxy/server/database/objects/f/3/d/dataset_f3d1ff58-dc18-49db-b4e4-db6176e0218b.dat' && mv fastq_out_r1_unpaired.'fastqsanger.gz' '/galaxy/server/database/objects/f/5/0/dataset_f50f33ad-1d07-4f0d-b25a-a7f8da385242.dat' && mv fastq_out_r2_paired.'fastqsanger.gz' '/galaxy/server/database/objects/3/9/1/dataset_391d572f-5ab9-4e2e-9ee3-ab4992b86b14.dat' && mv fastq_out_r2_unpaired.'fastqsanger.gz' '/galaxy/server/database/objects/7/3/8/dataset_738b4cb6-8c7c-41cf-978d-c535b76e59a5.dat'", "traceback": null, "params": {"readtype": "{\"__current_case__\": 1, \"fastq_r1_in\": {\"values\": [{\"id\": 17, \"src\": \"hda\"}]}, \"fastq_r2_in\": {\"values\": [{\"id\": 18, \"src\": \"hda\"}]}, \"single_or_paired\": \"pair_of_files\"}", "illuminaclip": "{\"__current_case__\": 1, \"do_illuminaclip\": false}", "operations": "[{\"__index__\": 0, \"operation\": {\"__current_case__\": 0, \"name\": \"SLIDINGWINDOW\", \"required_quality\": \"20\", \"window_size\": \"4\"}}]", "output_logs": "false", "output_err": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastqsanger.gz\""}, "inputs": {"readtype|fastq_r1_in": {"id": "c0c8a69c8070f677", "src": "hda", "uuid": "53530603-4b11-4771-b00f-55b679cdffef"}, "readtype|fastq_r2_in": {"id": "4a12ddb120e74961", "src": "hda", "uuid": "376767a6-2c00-4bc6-9292-29286bacc97d"}}, "outputs": {"fastq_out_r1_paired": {"id": "584d0aa45b50556b", "src": "hda", "uuid": "f3d1ff58-dc18-49db-b4e4-db6176e0218b"}, "fastq_out_r2_paired": {"id": "8b6f5ce3aa2377af", "src": "hda", "uuid": "391d572f-5ab9-4e2e-9ee3-ab4992b86b14"}, "fastq_out_r1_unpaired": {"id": "b4ed4b13837a07b8", "src": "hda", "uuid": "f50f33ad-1d07-4f0d-b25a-a7f8da385242"}, "fastq_out_r2_unpaired": {"id": "87943a4e2dd4167e", "src": "hda", "uuid": "738b4cb6-8c7c-41cf-978d-c535b76e59a5"}}, "output_collections": {}, "tool_stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticPE: Started with arguments:\n -threads 6 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz SLIDINGWINDOW:4:20\nQuality encoding detected as phred33\nInput Read Pairs: 10 Both Surviving: 8 (80.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 2 (20.00%) Dropped: 0 (0.00%)\nTrimmomaticPE: Completed successfully\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticPE: Started with arguments:\n -threads 6 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz SLIDINGWINDOW:4:20\nQuality encoding detected as phred33\nInput Read Pairs: 10 Both Surviving: 8 (80.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 2 (20.00%) Dropped: 0 (0.00%)\nTrimmomaticPE: Completed successfully\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}, {"title": "Memory Allocated (MB)", "value": "12884", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12884.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 00:53:41", "plugin": "core", "name": "start_epoch", "raw_value": "1726275221.0000000"}, {"title": "Job End Time", "value": "2024-09-14 00:53:41", "plugin": "core", "name": "end_epoch", "raw_value": "1726275221.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "trimmomatic/0.38.1-3", "has_data": true, "data": {"tool_id": "trimmomatic", "tool_version": "0.38.1", "test_index": 3, "time_seconds": 29.09535503387451, "inputs": {"readtype|fastq_r1_in": {"src": "hda", "id": "a6000a46566a855e"}, "readtype|fastq_r2_in": {"src": "hda", "id": "010a92ede45bd68a"}, "readtype|single_or_paired": "pair_of_files", "operations_0|operation|name": "SLIDINGWINDOW"}, "job": {"model_class": "Job", "id": "584d0aa45b50556b", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T00:54:19.702304", "create_time": "2024-09-14T00:54:08.999733", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-k4jps", "command_line": "if [ -z \"$TRIMMOMATIC_JAR_PATH\" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z \"$TRIMMOMATIC_ADAPTERS_PATH\" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/a/3/9/dataset_a399456d-910b-4145-8d59-78d9823e55eb.dat' fastq_r1.'fastqsanger' && ln -s '/galaxy/server/database/objects/9/7/6/dataset_9761247d-c9ae-48df-900f-53bd8cc116f1.dat' fastq_r2.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar PE -threads ${GALAXY_SLOTS:-6} fastq_r1.'fastqsanger' fastq_r2.'fastqsanger' fastq_out_r1_paired.'fastqsanger' fastq_out_r1_unpaired.'fastqsanger' fastq_out_r2_paired.'fastqsanger' fastq_out_r2_unpaired.'fastqsanger' SLIDINGWINDOW:4:20 2>&1 | tee trimmomatic.log && if [ -z \"$(tail -1 trimmomatic.log | grep \"Completed successfully\")\" ]; then echo \"Trimmomatic did not finish successfully\" >&2 ; exit 1 ; fi && mv fastq_out_r1_paired.'fastqsanger' '/galaxy/server/database/objects/f/4/9/dataset_f49461db-2aa7-4951-a7f8-5f1de529a7ba.dat' && mv fastq_out_r1_unpaired.'fastqsanger' '/galaxy/server/database/objects/e/e/8/dataset_ee808beb-2d67-4978-9f04-282d366f017a.dat' && mv fastq_out_r2_paired.'fastqsanger' '/galaxy/server/database/objects/9/c/e/dataset_9ce668de-b481-4e51-8d19-82fbcc93e8c9.dat' && mv fastq_out_r2_unpaired.'fastqsanger' '/galaxy/server/database/objects/c/d/e/dataset_cde3d066-4d48-4554-8895-ec108140037e.dat'", "traceback": null, "params": {"readtype": "{\"__current_case__\": 1, \"fastq_r1_in\": {\"values\": [{\"id\": 23, \"src\": \"hda\"}]}, \"fastq_r2_in\": {\"values\": [{\"id\": 24, \"src\": \"hda\"}]}, \"single_or_paired\": \"pair_of_files\"}", "illuminaclip": "{\"__current_case__\": 1, \"do_illuminaclip\": false}", "operations": "[{\"__index__\": 0, \"operation\": {\"__current_case__\": 0, \"name\": \"SLIDINGWINDOW\", \"required_quality\": \"20\", \"window_size\": \"4\"}}]", "output_logs": "false", "output_err": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastqsanger\""}, "inputs": {"readtype|fastq_r1_in": {"id": "a6000a46566a855e", "src": "hda", "uuid": "a399456d-910b-4145-8d59-78d9823e55eb"}, "readtype|fastq_r2_in": {"id": "010a92ede45bd68a", "src": "hda", "uuid": "9761247d-c9ae-48df-900f-53bd8cc116f1"}}, "outputs": {"fastq_out_r1_paired": {"id": "9d1e19ed450e6c86", "src": "hda", "uuid": "f49461db-2aa7-4951-a7f8-5f1de529a7ba"}, "fastq_out_r2_paired": {"id": "9bada2958fd12d58", "src": "hda", "uuid": "9ce668de-b481-4e51-8d19-82fbcc93e8c9"}, "fastq_out_r1_unpaired": {"id": "78f113974806f741", "src": "hda", "uuid": "ee808beb-2d67-4978-9f04-282d366f017a"}, "fastq_out_r2_unpaired": {"id": "877faa65ca7adf3a", "src": "hda", "uuid": "cde3d066-4d48-4554-8895-ec108140037e"}}, "output_collections": {}, "tool_stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticPE: Started with arguments:\n -threads 6 fastq_r1.fastqsanger fastq_r2.fastqsanger fastq_out_r1_paired.fastqsanger fastq_out_r1_unpaired.fastqsanger fastq_out_r2_paired.fastqsanger fastq_out_r2_unpaired.fastqsanger SLIDINGWINDOW:4:20\nQuality encoding detected as phred33\nInput Read Pairs: 10 Both Surviving: 8 (80.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 2 (20.00%) Dropped: 0 (0.00%)\nTrimmomaticPE: Completed successfully\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticPE: Started with arguments:\n -threads 6 fastq_r1.fastqsanger fastq_r2.fastqsanger fastq_out_r1_paired.fastqsanger fastq_out_r1_unpaired.fastqsanger fastq_out_r2_paired.fastqsanger fastq_out_r2_unpaired.fastqsanger SLIDINGWINDOW:4:20\nQuality encoding detected as phred33\nInput Read Pairs: 10 Both Surviving: 8 (80.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 2 (20.00%) Dropped: 0 (0.00%)\nTrimmomaticPE: Completed successfully\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}, {"title": "Memory Allocated (MB)", "value": "12884", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12884.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 00:54:11", "plugin": "core", "name": "start_epoch", "raw_value": "1726275251.0000000"}, {"title": "Job End Time", "value": "2024-09-14 00:54:11", "plugin": "core", "name": "end_epoch", "raw_value": "1726275251.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "trimmomatic/0.38.1-4", "has_data": true, "data": {"tool_id": "trimmomatic", "tool_version": "0.38.1", "test_index": 4, "time_seconds": 37.17274069786072, "inputs": {"readtype|fastq_r1_in": {"src": "hda", "id": "f7e63bf4200f2b12"}, "readtype|fastq_r2_in": {"src": "hda", "id": "64262c26ef4b4f8c"}, "readtype|single_or_paired": "pair_of_files", "operations_0|operation|name": "SLIDINGWINDOW"}, "job": {"model_class": "Job", "id": "87943a4e2dd4167e", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T00:54:56.858095", "create_time": "2024-09-14T00:54:46.461406", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-24xmf", "command_line": "if [ -z \"$TRIMMOMATIC_JAR_PATH\" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z \"$TRIMMOMATIC_ADAPTERS_PATH\" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/a/7/5/dataset_a754df7e-7666-4963-9680-c1eb2b89c689.dat' fastq_r1.'fastqillumina' && ln -s '/galaxy/server/database/objects/8/5/8/dataset_858a76de-2a92-4830-bf20-150923ad3cee.dat' fastq_r2.'fastqillumina' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar PE -threads ${GALAXY_SLOTS:-6} fastq_r1.'fastqillumina' fastq_r2.'fastqillumina' fastq_out_r1_paired.'fastqillumina' fastq_out_r1_unpaired.'fastqillumina' fastq_out_r2_paired.'fastqillumina' fastq_out_r2_unpaired.'fastqillumina' SLIDINGWINDOW:4:20 2>&1 | tee trimmomatic.log && if [ -z \"$(tail -1 trimmomatic.log | grep \"Completed successfully\")\" ]; then echo \"Trimmomatic did not finish successfully\" >&2 ; exit 1 ; fi && mv fastq_out_r1_paired.'fastqillumina' '/galaxy/server/database/objects/e/6/f/dataset_e6f68f70-9838-4b6c-9ab8-4d2f4ece8862.dat' && mv fastq_out_r1_unpaired.'fastqillumina' '/galaxy/server/database/objects/c/6/d/dataset_c6d8a8b3-4385-4bce-b0a1-1f6a777cbd6c.dat' && mv fastq_out_r2_paired.'fastqillumina' '/galaxy/server/database/objects/9/e/6/dataset_9e625eef-b2f0-4558-a53d-9ad9c770a633.dat' && mv fastq_out_r2_unpaired.'fastqillumina' '/galaxy/server/database/objects/d/1/d/dataset_d1de5762-2fca-4023-a70d-97380dd0d639.dat'", "traceback": null, "params": {"__input_ext": "\"fastqillumina\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_err": "false", "output_logs": "false", "operations": "[{\"__index__\": 0, \"operation\": {\"__current_case__\": 0, \"name\": \"SLIDINGWINDOW\", \"required_quality\": \"20\", \"window_size\": \"4\"}}]", "illuminaclip": "{\"__current_case__\": 1, \"do_illuminaclip\": false}", "readtype": "{\"__current_case__\": 1, \"fastq_r1_in\": {\"values\": [{\"id\": 29, \"src\": \"hda\"}]}, \"fastq_r2_in\": {\"values\": [{\"id\": 30, \"src\": \"hda\"}]}, \"single_or_paired\": \"pair_of_files\"}"}, "inputs": {"readtype|fastq_r1_in": {"id": "f7e63bf4200f2b12", "src": "hda", "uuid": "a754df7e-7666-4963-9680-c1eb2b89c689"}, "readtype|fastq_r2_in": {"id": "64262c26ef4b4f8c", "src": "hda", "uuid": "858a76de-2a92-4830-bf20-150923ad3cee"}}, "outputs": {"fastq_out_r1_paired": {"id": "f8ff9528d950258c", "src": "hda", "uuid": "e6f68f70-9838-4b6c-9ab8-4d2f4ece8862"}, "fastq_out_r1_unpaired": {"id": "7fd0ebaa51c36236", "src": "hda", "uuid": "c6d8a8b3-4385-4bce-b0a1-1f6a777cbd6c"}, "fastq_out_r2_unpaired": {"id": "da2d40552de3029b", "src": "hda", "uuid": "d1de5762-2fca-4023-a70d-97380dd0d639"}, "fastq_out_r2_paired": {"id": "fe9a443ac2bf50b7", "src": "hda", "uuid": "9e625eef-b2f0-4558-a53d-9ad9c770a633"}}, "output_collections": {}, "tool_stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticPE: Started with arguments:\n -threads 6 fastq_r1.fastqillumina fastq_r2.fastqillumina fastq_out_r1_paired.fastqillumina fastq_out_r1_unpaired.fastqillumina fastq_out_r2_paired.fastqillumina fastq_out_r2_unpaired.fastqillumina SLIDINGWINDOW:4:20\nQuality encoding detected as phred64\nInput Read Pairs: 10 Both Surviving: 8 (80.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 2 (20.00%) Dropped: 0 (0.00%)\nTrimmomaticPE: Completed successfully\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticPE: Started with arguments:\n -threads 6 fastq_r1.fastqillumina fastq_r2.fastqillumina fastq_out_r1_paired.fastqillumina fastq_out_r1_unpaired.fastqillumina fastq_out_r2_paired.fastqillumina fastq_out_r2_unpaired.fastqillumina SLIDINGWINDOW:4:20\nQuality encoding detected as phred64\nInput Read Pairs: 10 Both Surviving: 8 (80.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 2 (20.00%) Dropped: 0 (0.00%)\nTrimmomaticPE: Completed successfully\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}, {"title": "Memory Allocated (MB)", "value": "12884", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12884.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 00:54:47", "plugin": "core", "name": "start_epoch", "raw_value": "1726275287.0000000"}, {"title": "Job End Time", "value": "2024-09-14 00:54:48", "plugin": "core", "name": "end_epoch", "raw_value": "1726275288.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "trimmomatic/0.38.1-5", "has_data": true, "data": {"tool_id": "trimmomatic", "tool_version": "0.38.1", "test_index": 5, "time_seconds": 9.106432437896729, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "trimmomatic/0.38.1-6", "has_data": true, "data": {"tool_id": "trimmomatic", "tool_version": "0.38.1", "test_index": 6, "time_seconds": 24.780025243759155, "inputs": {"readtype|fastq_in": {"src": "hda", "id": "3e0e92ef37a541d1"}, "readtype|single_or_paired": "se", "operations_0|operation|crop": "10", "operations_0|operation|name": "CROP"}, "job": {"model_class": "Job", "id": "9bada2958fd12d58", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T00:55:33.562406", "create_time": "2024-09-14T00:55:23.878674", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-9q6rx", "command_line": "if [ -z \"$TRIMMOMATIC_JAR_PATH\" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z \"$TRIMMOMATIC_ADAPTERS_PATH\" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/5/5/f/dataset_55fff3a9-de72-43ff-9f76-a236277f93bd.dat' fastq_in.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger' fastq_out.'fastqsanger' CROP:10 2>&1 | tee trimmomatic.log && if [ -z \"$(tail -1 trimmomatic.log | grep \"Completed successfully\")\" ]; then echo \"Trimmomatic did not finish successfully\" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger' '/galaxy/server/database/objects/a/7/4/dataset_a742330e-6930-4420-9551-f2011b494d34.dat'", "traceback": null, "params": {"__input_ext": "\"fastqsanger\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_err": "false", "output_logs": "false", "operations": "[{\"__index__\": 0, \"operation\": {\"__current_case__\": 4, \"crop\": \"10\", \"name\": \"CROP\"}}]", "illuminaclip": "{\"__current_case__\": 1, \"do_illuminaclip\": false}", "readtype": "{\"__current_case__\": 0, \"fastq_in\": {\"values\": [{\"id\": 37, \"src\": \"hda\"}]}, \"single_or_paired\": \"se\"}"}, "inputs": {"readtype|fastq_in": {"id": "3e0e92ef37a541d1", "src": "hda", "uuid": "55fff3a9-de72-43ff-9f76-a236277f93bd"}}, "outputs": {"fastq_out": {"id": "4e6201563fcf9362", "src": "hda", "uuid": "a742330e-6930-4420-9551-f2011b494d34"}}, "output_collections": {}, "tool_stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticSE: Started with arguments:\n -threads 6 fastq_in.fastqsanger fastq_out.fastqsanger CROP:10\nQuality encoding detected as phred33\nInput Reads: 10 Surviving: 10 (100.00%) Dropped: 0 (0.00%)\nTrimmomaticSE: Completed successfully\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticSE: Started with arguments:\n -threads 6 fastq_in.fastqsanger fastq_out.fastqsanger CROP:10\nQuality encoding detected as phred33\nInput Reads: 10 Surviving: 10 (100.00%) Dropped: 0 (0.00%)\nTrimmomaticSE: Completed successfully\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}, {"title": "Memory Allocated (MB)", "value": "12884", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12884.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 00:55:25", "plugin": "core", "name": "start_epoch", "raw_value": "1726275325.0000000"}, {"title": "Job End Time", "value": "2024-09-14 00:55:25", "plugin": "core", "name": "end_epoch", "raw_value": "1726275325.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "trimmomatic/0.38.1-7", "has_data": true, "data": {"tool_id": "trimmomatic", "tool_version": "0.38.1", "test_index": 7, "time_seconds": 16.701301097869873, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "trimmomatic/0.38.1-8", "has_data": true, "data": {"tool_id": "trimmomatic", "tool_version": "0.38.1", "test_index": 8, "time_seconds": 14.641294717788696, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "trimmomatic/0.38.1-9", "has_data": true, "data": {"tool_id": "trimmomatic", "tool_version": "0.38.1", "test_index": 9, "time_seconds": 26.865060567855835, "inputs": {"readtype|fastq_in": {"src": "hda", "id": "c1f53f965e3f11fc"}, "readtype|single_or_paired": "se", "operations_0|operation|avgqual": "30", "operations_0|operation|name": "AVGQUAL"}, "job": {"model_class": "Job", "id": "fe9a443ac2bf50b7", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T00:56:32.211720", "create_time": "2024-09-14T00:56:21.731302", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1", "history_id": "ed165837e8ba4cca", "external_id": "gxy-wnc6s", "command_line": "if [ -z \"$TRIMMOMATIC_JAR_PATH\" ]; then export TRIMMOMATIC_JAR_PATH=$(dirname $(readlink -e $(which trimmomatic))); fi && if [ -z \"$TRIMMOMATIC_ADAPTERS_PATH\" ]; then export TRIMMOMATIC_ADAPTERS_PATH=$(dirname $(readlink -e $(which trimmomatic)))/adapters; fi && ln -s '/galaxy/server/database/objects/8/1/3/dataset_813b5365-28a5-418e-a20e-6b04f7f61870.dat' fastq_in.'fastqsanger' && java ${_JAVA_OPTIONS:--Xmx8G} -jar $TRIMMOMATIC_JAR_PATH/trimmomatic.jar SE -threads ${GALAXY_SLOTS:-6} fastq_in.'fastqsanger' fastq_out.'fastqsanger' AVGQUAL:30 2>&1 | tee trimmomatic.log && if [ -z \"$(tail -1 trimmomatic.log | grep \"Completed successfully\")\" ]; then echo \"Trimmomatic did not finish successfully\" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger' '/galaxy/server/database/objects/5/5/0/dataset_550be6c4-6a57-46b0-918e-0aacda978dd7.dat'", "traceback": null, "params": {"readtype": "{\"__current_case__\": 0, \"fastq_in\": {\"values\": [{\"id\": 43, \"src\": \"hda\"}]}, \"single_or_paired\": \"se\"}", "illuminaclip": "{\"__current_case__\": 1, \"do_illuminaclip\": false}", "operations": "[{\"__index__\": 0, \"operation\": {\"__current_case__\": 6, \"avgqual\": \"30\", \"name\": \"AVGQUAL\"}}]", "output_logs": "false", "output_err": "false", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastqsanger\""}, "inputs": {"readtype|fastq_in": {"id": "c1f53f965e3f11fc", "src": "hda", "uuid": "813b5365-28a5-418e-a20e-6b04f7f61870"}}, "outputs": {"fastq_out": {"id": "f77b84ee3fc05e8c", "src": "hda", "uuid": "550be6c4-6a57-46b0-918e-0aacda978dd7"}}, "output_collections": {}, "tool_stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticSE: Started with arguments:\n -threads 6 fastq_in.fastqsanger fastq_out.fastqsanger AVGQUAL:30\nQuality encoding detected as phred33\nInput Reads: 10 Surviving: 4 (40.00%) Dropped: 6 (60.00%)\nTrimmomaticSE: Completed successfully\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Picked up _JAVA_OPTIONS: -Xmx12G -Xms1G\nTrimmomaticSE: Started with arguments:\n -threads 6 fastq_in.fastqsanger fastq_out.fastqsanger AVGQUAL:30\nQuality encoding detected as phred33\nInput Reads: 10 Surviving: 4 (40.00%) Dropped: 6 (60.00%)\nTrimmomaticSE: Completed successfully\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "6", "plugin": "core", "name": "galaxy_slots", "raw_value": "6.0000000"}, {"title": "Memory Allocated (MB)", "value": "12884", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12884.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 00:56:23", "plugin": "core", "name": "start_epoch", "raw_value": "1726275383.0000000"}, {"title": "Job End Time", "value": "2024-09-14 00:56:24", "plugin": "core", "name": "end_epoch", "raw_value": "1726275384.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "vcfbreakcreatemulti/1.0.0_rc3+galaxy0-0", "has_data": true, "data": {"tool_id": "vcfbreakcreatemulti", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 0, "time_seconds": 29.375492334365845, "inputs": {"input1": {"src": "hda", "id": "6866e8eee2e30678"}, "break_or_create": "break"}, "job": {"model_class": "Job", "id": "e5e85752534a1f6b", "state": "ok", "exit_code": 0, "update_time": "2024-09-14T01:07:07.133859", "create_time": "2024-09-14T01:06:53.320423", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": 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"\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "vcf_samples": "[\"NA00001\", \"NA00003\"]"}, "inputs": {"input1": {"id": "251b4eb87d395ff4", "src": "hda", "uuid": "84e39377-0100-40a9-ba12-9ca6dd14878f"}}, "outputs": {"out_file1": {"id": "22470166765b2f95", "src": "hda", "uuid": "42df1ec7-6bca-4aed-8966-66ea16ac07bf"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-14 01:07:54", "plugin": "core", "name": "end_epoch", "raw_value": "1726276074.0000000"}, {"title": "Job Start Time", "value": "2024-09-14 01:07:54", "plugin": "core", "name": "start_epoch", "raw_value": "1726276074.0000000"}, {"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://34.74.20.157:8000/galaxy/"} \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/results.xunit b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/results.xunit new file mode 100644 index 000000000..9397b1058 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/results.xunit @@ -0,0 +1,704 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0contig count: 24 element count: 19592 complex nodes: 0# of ones in rank vector: 23[2024-09-14 01:13:29.550] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.[2024-09-14 01:13:29.550] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./indexsize = 19592-----------------------------------------| Loading contigs | Time = 1.3544 ms-----------------------------------------size = 19592-----------------------------------------| Loading contig boundaries | Time = 858.55 us-----------------------------------------Number of ones: 23Number of ones per inventory item: 512Inventory entries filled: 123[2024-09-14 01:13:29.552] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.[2024-09-14 01:13:29.552] [puff::index::jointLog] [info] contig count for validation: 23[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] Total # of Contigs : 23[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] Total # of numerical Contigs : 23[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] Total # of contig vec entries: 36[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] bits per offset entry 6[2024-09-14 01:13:29.553] [puff::index::jointLog] [info] Done constructing the contig vector. 24[2024-09-14 01:13:29.564] [puff::index::jointLog] [info] # segments = 23[2024-09-14 01:13:29.564] [puff::index::jointLog] [info] total length = 19592[2024-09-14 01:13:29.564] [puff::index::jointLog] [info] Reading the reference files ...[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] positional integer width = 15[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] seqSize = 19592[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] rankSize = 19592[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] edgeVecSize = 0[2024-09-14 01:13:29.575] [puff::index::jointLog] [info] num keys = 18902[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % 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remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[2024-09-14 01:13:29.659] [puff::index::jointLog] [info] mphf size = 0.0125198 MB[2024-09-14 01:13:29.659] [puff::index::jointLog] [info] chunk size = 9796[2024-09-14 01:13:29.659] [puff::index::jointLog] [info] chunk 0 = [0, 9796)[2024-09-14 01:13:29.659] [puff::index::jointLog] [info] chunk 1 = [9796, 19562)[2024-09-14 01:13:29.660] [puff::index::jointLog] [info] finished populating pos vector[2024-09-14 01:13:29.660] [puff::index::jointLog] [info] writing index components[2024-09-14 01:13:29.674] [puff::index::jointLog] [info] finished writing dense pufferfish index[2024-09-14 01:13:29.681] [jLog] [info] done building indexVersion Info: ### PLEASE UPGRADE SALMON ###### A newer version of salmon with important bug fixes and improvements is available. #######The newest version, available at https://github.com/COMBINE-lab/salmon/releasescontains new features, improvements, and bug fixes; please upgrade at yourearliest convenience.###Sign up for the salmon mailing list to hear about new versions, features and updates at:https://oceangenomics.com/subscribe###### salmon (selective-alignment-based) v1.3.0### [ program ] => salmon ### [ command ] => quant ### [ index ] => { ./index }### [ libType ] => { U }### [ unmatedReads ] => { ./single.fasta }### [ threads ] => { 6 }### [ writeMappings ] => { ./output/samout.sam }### [ incompatPrior ] => { 0.0 }### [ biasSpeedSamp ] => { 5 }### [ fldMax ] => { 1000 }### [ fldMean ] => { 250 }### [ fldSD ] => { 25 }### [ forgettingFactor ] => { 0.65 }### [ maxReadOcc ] => { 100 }### [ numBiasSamples ] => { 2000000 }### [ numAuxModelSamples ] => { 5000000 }### [ numPreAuxModelSamples ] => { 5000 }### [ numGibbsSamples ] => { 0 }### [ numBootstraps ] => { 0 }### [ thinningFactor ] => { 16 }### [ sigDigits ] => { 3 }### [ vbPrior ] => { 1e-05 }### [ output ] => { ./output }Logs will be written to ./output/logs[2024-09-14 01:13:30.154] [jointLog] [info] setting maxHashResizeThreads to 6[2024-09-14 01:13:30.154] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.[2024-09-14 01:13:30.154] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65[2024-09-14 01:13:30.154] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.[2024-09-14 01:13:30.154] [jointLog] [info] parsing read library format[2024-09-14 01:13:30.154] [jointLog] [info] There is 1 library.-----------------------------------------| Loading contig table | Time = 965.86 us-----------------------------------------size = 24-----------------------------------------| Loading contig offsets | Time = 1.6044 ms----------------------------------------------------------------------------------| Loading reference lengths | Time = 715.63 us-----------------------------------------[2024-09-14 01:13:30.248] [jointLog] [info] Loading pufferfish index[2024-09-14 01:13:30.249] [jointLog] [info] Loading dense pufferfish index.-----------------------------------------| Loading mphf table | Time = 802.15 us-----------------------------------------size = 19592Number of ones: 23Number of ones per inventory item: 512Inventory entries filled: 1-----------------------------------------| Loading contig boundaries | Time = 1.1211 ms-----------------------------------------size = 19592-----------------------------------------| Loading sequence | Time = 792.46 us-----------------------------------------size = 18902-----------------------------------------| Loading positions | Time = 1.5093 ms-----------------------------------------size = 28562-----------------------------------------| Loading reference sequence | Time = 737.14 us----------------------------------------------------------------------------------| Loading reference accumulative lengths | Time = 430.98 us-----------------------------------------[2024-09-14 01:13:30.260] [jointLog] [info] done[2024-09-14 01:13:30.260] [jointLog] [info] Index contained 15 targets[2024-09-14 01:13:30.260] [jointLog] [info] Number of decoys : 0[2024-09-14 01:13:30.307] [jointLog] [info] Computed 15 rich equivalence classes for further processing[2024-09-14 01:13:30.307] [jointLog] [info] Counted 15 total reads in the equivalence classes [2024-09-14 01:13:30.308] [jointLog] [info] Number of mappings discarded because of alignment score : 5[2024-09-14 01:13:30.308] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0[2024-09-14 01:13:30.308] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0[2024-09-14 01:13:30.308] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0[2024-09-14 01:13:30.308] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.The effective lengths have been computed using the observed mappings.[2024-09-14 01:13:30.308] [jointLog] [info] Mapping rate = 100%[2024-09-14 01:13:30.308] [jointLog] [info] finished quantifyLibrary()[2024-09-14 01:13:30.313] [jointLog] [info] Starting optimizer[2024-09-14 01:13:30.313] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate[2024-09-14 01:13:30.313] [jointLog] [info] iteration = 0 | max rel diff. = 0[2024-09-14 01:13:30.314] [jointLog] [info] iteration = 100 | max rel diff. = 0[2024-09-14 01:13:30.315] [jointLog] [info] Finished optimizer[2024-09-14 01:13:30.315] [jointLog] [info] writing output [2024-09-14 01:13:30.319] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :Detected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details + ]]> + + + + + + + + 1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0contig count: 24 element count: 19592 complex nodes: 0# of ones in rank vector: 23[2024-09-14 01:14:01.952] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.[2024-09-14 01:14:01.952] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./indexsize = 19592-----------------------------------------| Loading contigs | Time = 1.8348 ms-----------------------------------------size = 19592-----------------------------------------| Loading contig boundaries | Time = 1.0511 ms-----------------------------------------Number of ones: 23Number of ones per inventory item: 512Inventory entries filled: 123[2024-09-14 01:14:01.955] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.[2024-09-14 01:14:01.955] [puff::index::jointLog] [info] contig count for validation: 23[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] Total # of Contigs : 23[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] Total # of numerical Contigs : 23[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] Total # of contig vec entries: 36[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] bits per offset entry 6[2024-09-14 01:14:01.956] [puff::index::jointLog] [info] Done constructing the contig vector. 24[2024-09-14 01:14:01.970] [puff::index::jointLog] [info] # segments = 23[2024-09-14 01:14:01.970] [puff::index::jointLog] [info] total length = 19592[2024-09-14 01:14:01.970] [puff::index::jointLog] [info] Reading the reference files ...[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] positional integer width = 15[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] seqSize = 19592[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] rankSize = 19592[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] edgeVecSize = 0[2024-09-14 01:14:01.982] [puff::index::jointLog] [info] num keys = 18902[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec 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elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[2024-09-14 01:14:02.084] [puff::index::jointLog] [info] mphf size = 0.0125198 MB[2024-09-14 01:14:02.084] [puff::index::jointLog] [info] chunk size = 9796[2024-09-14 01:14:02.084] [puff::index::jointLog] [info] chunk 0 = [0, 9796)[2024-09-14 01:14:02.084] [puff::index::jointLog] [info] chunk 1 = [9796, 19562)[2024-09-14 01:14:02.085] [puff::index::jointLog] [info] finished populating pos vector[2024-09-14 01:14:02.085] [puff::index::jointLog] [info] writing index components[2024-09-14 01:14:02.100] [puff::index::jointLog] [info] finished writing dense pufferfish index[2024-09-14 01:14:02.107] [jLog] [info] done building indexVersion Info: ### PLEASE UPGRADE SALMON ###### A newer version of salmon with important bug fixes and improvements is available. #######The newest version, available at https://github.com/COMBINE-lab/salmon/releasescontains new features, improvements, and bug fixes; please upgrade at yourearliest convenience.###Sign up for the salmon mailing list to hear about new versions, features and updates at:https://oceangenomics.com/subscribe###### salmon (selective-alignment-based) v1.3.0### [ program ] => salmon ### [ command ] => quant ### [ index ] => { ./index }### [ libType ] => { U }### [ unmatedReads ] => { ./single.fasta }### [ threads ] => { 6 }### [ incompatPrior ] => { 0.0 }### [ biasSpeedSamp ] => { 5 }### [ fldMax ] => { 1000 }### [ fldMean ] => { 250 }### [ fldSD ] => { 25 }### [ forgettingFactor ] => { 0.65 }### [ maxReadOcc ] => { 100 }### [ numBiasSamples ] => { 2000000 }### [ numAuxModelSamples ] => { 5000000 }### [ numPreAuxModelSamples ] => { 5000 }### [ numGibbsSamples ] => { 0 }### [ numBootstraps ] => { 0 }### [ thinningFactor ] => { 16 }### [ sigDigits ] => { 3 }### [ vbPrior ] => { 1e-05 }### [ output ] => { ./output }Logs will be written to ./output/logs[2024-09-14 01:14:02.202] [jointLog] [info] setting maxHashResizeThreads to 6[2024-09-14 01:14:02.202] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.[2024-09-14 01:14:02.202] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65[2024-09-14 01:14:02.202] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.[2024-09-14 01:14:02.202] [jointLog] [info] parsing read library format[2024-09-14 01:14:02.202] [jointLog] [info] There is 1 library.-----------------------------------------| Loading contig table | Time = 1.1905 ms-----------------------------------------size = 24-----------------------------------------| Loading contig offsets | Time = 1.7182 ms----------------------------------------------------------------------------------| Loading reference lengths | Time = 564.82 us----------------------------------------------------------------------------------| Loading mphf table | Time = 1.2042 ms-----------------------------------------size = 19592Number of ones: 23Number of ones per inventory item: 512Inventory entries filled: 1-----------------------------------------| Loading contig boundaries | Time = 1.1029 ms-----------------------------------------size = 19592-----------------------------------------| Loading sequence | Time = 952.18 us-----------------------------------------size = 18902-----------------------------------------| Loading positions | Time = 1.5979 ms-----------------------------------------size = 28562-----------------------------------------| Loading reference sequence | Time = 803.94 us----------------------------------------------------------------------------------| Loading reference accumulative lengths | Time = 595.88 us-----------------------------------------[2024-09-14 01:14:02.288] [jointLog] [info] Loading pufferfish index[2024-09-14 01:14:02.289] [jointLog] [info] Loading dense pufferfish index.[2024-09-14 01:14:02.301] [jointLog] [info] done[2024-09-14 01:14:02.301] [jointLog] [info] Index contained 15 targets[2024-09-14 01:14:02.301] [jointLog] [info] Number of decoys : 0[2024-09-14 01:14:02.348] [jointLog] [info] Computed 15 rich equivalence classes for further processing[2024-09-14 01:14:02.348] [jointLog] [info] Counted 15 total reads in the equivalence classes [2024-09-14 01:14:02.349] [jointLog] [info] Number of mappings discarded because of alignment score : 5[2024-09-14 01:14:02.349] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0[2024-09-14 01:14:02.349] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0[2024-09-14 01:14:02.349] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0[2024-09-14 01:14:02.350] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.The effective lengths have been computed using the observed mappings.[2024-09-14 01:14:02.350] [jointLog] [info] Mapping rate = 100%[2024-09-14 01:14:02.350] [jointLog] [info] finished quantifyLibrary()[2024-09-14 01:14:02.354] [jointLog] [info] Starting optimizer[2024-09-14 01:14:02.355] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate[2024-09-14 01:14:02.355] [jointLog] [info] iteration = 0 | max rel diff. = 0[2024-09-14 01:14:02.356] [jointLog] [info] iteration = 100 | max rel diff. = 0[2024-09-14 01:14:02.357] [jointLog] [info] Finished optimizer[2024-09-14 01:14:02.357] [jointLog] [info] writing output [2024-09-14 01:14:02.362] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :Detected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details + ]]> + + + + + + + + 1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0contig count: 24 element count: 19592 complex nodes: 0# of ones in rank vector: 23[2024-09-14 01:14:30.555] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.[2024-09-14 01:14:30.555] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./indexsize = 19592-----------------------------------------| Loading contigs | Time = 1.3885 ms-----------------------------------------size = 19592-----------------------------------------| Loading contig boundaries | Time = 995.27 us-----------------------------------------Number of ones: 23Number of ones per inventory item: 512Inventory entries filled: 123[2024-09-14 01:14:30.558] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.[2024-09-14 01:14:30.558] [puff::index::jointLog] [info] contig count for validation: 23[2024-09-14 01:14:30.558] [puff::index::jointLog] [info] Total # of Contigs : 23[2024-09-14 01:14:30.558] [puff::index::jointLog] [info] Total # of numerical Contigs : 23[2024-09-14 01:14:30.559] [puff::index::jointLog] [info] Total # of contig vec entries: 36[2024-09-14 01:14:30.559] [puff::index::jointLog] [info] bits per offset entry 6[2024-09-14 01:14:30.559] [puff::index::jointLog] [info] Done constructing the contig vector. 24[2024-09-14 01:14:30.570] [puff::index::jointLog] [info] # segments = 23[2024-09-14 01:14:30.570] [puff::index::jointLog] [info] total length = 19592[2024-09-14 01:14:30.570] [puff::index::jointLog] [info] Reading the reference files ...[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] positional integer width = 15[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] seqSize = 19592[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] rankSize = 19592[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] edgeVecSize = 0[2024-09-14 01:14:30.581] [puff::index::jointLog] [info] num keys = 18902[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec 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elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[2024-09-14 01:14:30.661] [puff::index::jointLog] [info] mphf size = 0.0125198 MB[2024-09-14 01:14:30.661] [puff::index::jointLog] [info] chunk size = 9796[2024-09-14 01:14:30.661] [puff::index::jointLog] [info] chunk 0 = [0, 9796)[2024-09-14 01:14:30.661] [puff::index::jointLog] [info] chunk 1 = [9796, 19562)[2024-09-14 01:14:30.662] [puff::index::jointLog] [info] finished populating pos vector[2024-09-14 01:14:30.662] [puff::index::jointLog] [info] writing index components[2024-09-14 01:14:30.675] [puff::index::jointLog] [info] finished writing dense pufferfish index[2024-09-14 01:14:30.681] [jLog] [info] done building indexVersion Info: ### PLEASE UPGRADE SALMON ###### A newer version of salmon with important bug fixes and improvements is available. #######The newest version, available at https://github.com/COMBINE-lab/salmon/releasescontains new features, improvements, and bug fixes; please upgrade at yourearliest convenience.###Sign up for the salmon mailing list to hear about new versions, features and updates at:https://oceangenomics.com/subscribe###### salmon (selective-alignment-based) v1.3.0### [ program ] => salmon ### [ command ] => quant ### [ index ] => { ./index }### [ libType ] => { U }### [ unmatedReads ] => { ./single.fasta }### [ threads ] => { 6 }### [ incompatPrior ] => { 0.0 }### [ biasSpeedSamp ] => { 5 }### [ fldMax ] => { 1000 }### [ fldMean ] => { 250 }### [ fldSD ] => { 25 }### [ forgettingFactor ] => { 0.65 }### [ maxReadOcc ] => { 100 }### [ numBiasSamples ] => { 2000000 }### [ numAuxModelSamples ] => { 5000000 }### [ numPreAuxModelSamples ] => { 5000 }### [ numGibbsSamples ] => { 0 }### [ numBootstraps ] => { 0 }### [ thinningFactor ] => { 16 }### [ sigDigits ] => { 3 }### [ vbPrior ] => { 1e-05 }### [ output ] => { ./output }Logs will be written to ./output/logs[2024-09-14 01:14:30.759] [jointLog] [info] setting maxHashResizeThreads to 6[2024-09-14 01:14:30.759] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.[2024-09-14 01:14:30.759] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65[2024-09-14 01:14:30.759] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.[2024-09-14 01:14:30.759] [jointLog] [info] parsing read library format[2024-09-14 01:14:30.759] [jointLog] [info] There is 1 library.-----------------------------------------| Loading contig table | Time = 1.2042 ms-----------------------------------------size = 24-----------------------------------------| Loading contig offsets | Time = 1.5305 ms----------------------------------------------------------------------------------| Loading reference lengths | Time = 697.75 us----------------------------------------------------------------------------------| Loading mphf table | Time = 505.56 us-----------------------------------------size = 19592Number of ones: 23Number of ones per inventory item: 512Inventory entries filled: 1-----------------------------------------| Loading contig boundaries | Time = 908.85 us-----------------------------------------size = 19592-----------------------------------------| Loading sequence | Time = 1.0946 ms-----------------------------------------size = 18902-----------------------------------------| Loading positions | Time = 1.4588 ms-----------------------------------------size = 28562-----------------------------------------| Loading reference sequence | Time = 1.0765 ms----------------------------------------------------------------------------------| Loading reference accumulative lengths | Time = 668.87 us-----------------------------------------[2024-09-14 01:14:30.845] [jointLog] [info] Loading pufferfish index[2024-09-14 01:14:30.847] [jointLog] [info] Loading dense pufferfish index.[2024-09-14 01:14:30.858] [jointLog] [info] done[2024-09-14 01:14:30.858] [jointLog] [info] Index contained 15 targets[2024-09-14 01:14:30.858] [jointLog] [info] Number of decoys : 0[2024-09-14 01:14:30.905] [jointLog] [info] Computed 15 rich equivalence classes for further processing[2024-09-14 01:14:30.905] [jointLog] [info] Counted 15 total reads in the equivalence classes [2024-09-14 01:14:30.906] [jointLog] [info] Number of mappings discarded because of alignment score : 5[2024-09-14 01:14:30.906] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0[2024-09-14 01:14:30.906] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0[2024-09-14 01:14:30.906] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0[2024-09-14 01:14:30.906] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.The effective lengths have been computed using the observed mappings.[2024-09-14 01:14:30.906] [jointLog] [info] Mapping rate = 100%[2024-09-14 01:14:30.906] [jointLog] [info] finished quantifyLibrary()[2024-09-14 01:14:30.911] [jointLog] [info] Starting optimizer[2024-09-14 01:14:30.911] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate[2024-09-14 01:14:30.911] [jointLog] [info] iteration = 0 | max rel diff. = 0[2024-09-14 01:14:30.913] [jointLog] [info] iteration = 100 | max rel diff. = 0[2024-09-14 01:14:30.913] [jointLog] [info] Finished optimizer[2024-09-14 01:14:30.913] [jointLog] [info] writing output [2024-09-14 01:14:30.918] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :Detected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details + ]]> + + + + + + + + + + salmon # [ command ] => quant # [ targets ] => { /galaxy/server/database/objects/3/f/9/dataset_3f98742b-13bf-4a63-b43c-e12943fc60b3.dat }# [ libType ] => { U }# [ alignments ] => { /galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat }# [ threads ] => { 6 }# [ noErrorModel ] => { }# [ numErrorBins ] => { 5 }# [ sampleOut ] => { }# [ sampleUnaligned ] => { }# [ incompatPrior ] => { 0.0 }# [ biasSpeedSamp ] => { 5 }# [ fldMax ] => { 1000 }# [ fldMean ] => { 250 }# [ fldSD ] => { 25 }# [ forgettingFactor ] => { 0.65 }# [ maxReadOcc ] => { 100 }# [ numBiasSamples ] => { 2000000 }# [ numAuxModelSamples ] => { 5000000 }# [ numPreAuxModelSamples ] => { 5000 }# [ numGibbsSamples ] => { 0 }# [ numBootstraps ] => { 0 }# [ thinningFactor ] => { 16 }# [ sigDigits ] => { 3 }# [ vbPrior ] => { 1e-05 }# [ output ] => { ./output }Logs will be written to ./output/logs[2024-09-14 01:15:00.963] [jointLog] [info] setting maxHashResizeThreads to 6[2024-09-14 01:15:00.963] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.Library format { type:single end, relative orientation:none, strandedness:unstranded }[2024-09-14 01:15:00.965] [jointLog] [info] numQuantThreads = 3parseThreads = 3Checking that provided alignment files have consistent headers . . . donePopulating targets from aln = "/galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat", fasta = "/galaxy/server/database/objects/3/f/9/dataset_3f98742b-13bf-4a63-b43c-e12943fc60b3.dat" . . .done[0;32mprocessed[0;31m 0 [0;32mreads in current round[0;0m[0;32mprocessed[0;31m 28503 [0;32mreads in current round[0;0mkilling thread 0 . . . donekilling thread 1 . . . donekilling thread 2 . . . done# observed = 28503 / # required = 50000000[A[A[A[A[AResetting BAMQueue from file(s) [ "/galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat" ] . . . done[32mprocessed[31m 0 [32mreads[0mkilling thread 0 . . . donekilling thread 1 . . . donekilling thread 2 . . . done# observed = 28503 mapped fragments.[F[F[F[FWaiting on output threaddoneFreeing memory used by read queue . . . Joined parsing thread . . . "/galaxy/server/database/objects/c/c/6/dataset_cc6c1385-feae-4b8f-9391-4715d9c69c89.dat" Closed all files . . . [2024-09-14 01:15:01.340] [jointLog] [info] replaced 0 non-ACGT nucleotides with random nucleotides[2024-09-14 01:15:01.515] [jointLog] [info] Completed first pass through the alignment file.Total # of mapped reads : 28503# of uniquely mapped reads : 28502# ambiguously mapped reads : 1[2024-09-14 01:15:01.519] [jointLog] [info] Computed 18 rich equivalence classes for further processing[2024-09-14 01:15:01.519] [jointLog] [info] Counted 28503 total reads in the equivalence classes [2024-09-14 01:15:01.519] [jointLog] [warning] Only 28503 fragments were mapped, but the number of burn-in fragments was set to 5000000.The effective lengths have been computed using the observed mappings.[2024-09-14 01:15:01.521] [jointLog] [info] starting optimizer[2024-09-14 01:15:01.521] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate[2024-09-14 01:15:01.521] [jointLog] [info] iteration = 0 | max rel diff. = 21.8815[2024-09-14 01:15:01.523] [jointLog] [info] iteration = 100 | max rel diff. = 0[2024-09-14 01:15:01.523] [jointLog] [info] finished optimizer[2024-09-14 01:15:01.523] [jointLog] [info] writing output[2024-09-14 01:15:01.528] [jointLog] [info] Sampling alignments; outputting results to ./output/postSample.bamEmptied frag queue. . . Emptied Alignemnt Group Pool. . Emptied Alignment Group Queue. . . done[bam_sort_core] merging from 0 files and 6 in-memory blocks... + ]]> + + + + + + + + 1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0contig count: 24 element count: 19592 complex nodes: 0# of ones in rank vector: 23[2024-09-14 01:15:29.625] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.[2024-09-14 01:15:29.625] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./indexsize = 19592-----------------------------------------| Loading contigs | Time = 1.2944 ms-----------------------------------------size = 19592-----------------------------------------| Loading contig boundaries | Time = 718.91 us-----------------------------------------Number of ones: 23Number of ones per inventory item: 512Inventory entries filled: 123[2024-09-14 01:15:29.627] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.[2024-09-14 01:15:29.627] [puff::index::jointLog] [info] contig count for validation: 23[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] Total # of Contigs : 23[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] Total # of numerical Contigs : 23[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] Total # of contig vec entries: 36[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] bits per offset entry 6[2024-09-14 01:15:29.628] [puff::index::jointLog] [info] Done constructing the contig vector. 24[2024-09-14 01:15:29.639] [puff::index::jointLog] [info] # segments = 23[2024-09-14 01:15:29.639] [puff::index::jointLog] [info] total length = 19592[2024-09-14 01:15:29.639] [puff::index::jointLog] [info] Reading the reference files ...[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] positional integer width = 15[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] seqSize = 19592[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] rankSize = 19592[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] edgeVecSize = 0[2024-09-14 01:15:29.648] [puff::index::jointLog] [info] num keys = 18902[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 2.32 % elapsed: 0 min 0 sec 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[puff::index::jointLog] [info] chunk 1 = [9796, 19562)[2024-09-14 01:15:29.737] [puff::index::jointLog] [info] finished populating pos vector[2024-09-14 01:15:29.737] [puff::index::jointLog] [info] writing index components[2024-09-14 01:15:29.751] [puff::index::jointLog] [info] finished writing dense pufferfish index[2024-09-14 01:15:29.757] [jLog] [info] done building indexVersion Info: ### PLEASE UPGRADE SALMON ###### A newer version of salmon with important bug fixes and improvements is available. #######The newest version, available at https://github.com/COMBINE-lab/salmon/releasescontains new features, improvements, and bug fixes; please upgrade at yourearliest convenience.###Sign up for the salmon mailing list to hear about new versions, features and updates at:https://oceangenomics.com/subscribe###### salmon (selective-alignment-based) v1.3.0### [ program ] => salmon ### [ command ] => quant ### [ index ] => { ./index }### [ libType ] => { U }### [ unmatedReads ] => { ./single.fasta }### [ threads ] => { 6 }### [ validateMappings ] => { }### [ minScoreFraction ] => { 0.65 }### [ ma ] => { 2 }### [ mp ] => { 4 }### [ go ] => { 5 }### [ ge ] => { 3 }### [ allowDovetail ] => { }### [ recoverOrphans ] => { }### [ incompatPrior ] => { 0.0 }### [ biasSpeedSamp ] => { 5 }### [ fldMax ] => { 1000 }### [ fldMean ] => { 250 }### [ fldSD ] => { 25 }### [ forgettingFactor ] => { 0.65 }### [ maxReadOcc ] => { 100 }### [ numBiasSamples ] => { 2000000 }### [ numAuxModelSamples ] => { 5000000 }### [ numPreAuxModelSamples ] => { 5000 }### [ numGibbsSamples ] => { 0 }### [ numBootstraps ] => { 0 }### [ thinningFactor ] => { 16 }### [ sigDigits ] => { 3 }### [ vbPrior ] => { 1e-05 }### [ output ] => { ./output }Logs will be written to ./output/logs[2024-09-14 01:15:29.961] [jointLog] [info] setting maxHashResizeThreads to 6[2024-09-14 01:15:29.961] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.[2024-09-14 01:15:29.961] [jointLog] [warning] You set the mismatch penalty as 4, but it should be negative. It is being negated to -4.[2024-09-14 01:15:29.961] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.[2024-09-14 01:15:29.961] [jointLog] [info] parsing read library format[2024-09-14 01:15:29.961] [jointLog] [info] There is 1 library.-----------------------------------------| Loading contig table | Time = 1.1164 ms-----------------------------------------size = 24-----------------------------------------| Loading contig offsets | Time = 2.1175 ms----------------------------------------------------------------------------------| Loading reference lengths | Time = 750.63 us----------------------------------------------------------------------------------| Loading mphf table | Time = 943.23 us-----------------------------------------size = 19592Number of ones: 23Number of ones per inventory item: 512Inventory entries filled: 1-----------------------------------------| Loading contig boundaries | Time = 1.1738 ms-----------------------------------------size = 19592-----------------------------------------| Loading sequence | Time = 1.2531 ms-----------------------------------------[2024-09-14 01:15:30.051] [jointLog] [info] Loading pufferfish index[2024-09-14 01:15:30.052] [jointLog] [info] Loading dense pufferfish index.size = 18902-----------------------------------------| Loading positions | Time = 1.6923 ms-----------------------------------------size = 28562-----------------------------------------| Loading reference sequence | Time = 848.79 us----------------------------------------------------------------------------------| Loading reference accumulative lengths | Time = 571.89 us-----------------------------------------[2024-09-14 01:15:30.065] [jointLog] [info] done[2024-09-14 01:15:30.065] [jointLog] [info] Index contained 15 targets[2024-09-14 01:15:30.065] [jointLog] [info] Number of decoys : 0[2024-09-14 01:15:30.112] [jointLog] [info] Computed 15 rich equivalence classes for further processing[2024-09-14 01:15:30.112] [jointLog] [info] Counted 15 total reads in the equivalence classes [2024-09-14 01:15:30.114] [jointLog] [info] Number of orphans recovered using orphan rescue : 0[2024-09-14 01:15:30.114] [jointLog] [info] Number of mappings discarded because of alignment score : 6[2024-09-14 01:15:30.114] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0[2024-09-14 01:15:30.114] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0[2024-09-14 01:15:30.114] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.The effective lengths have been computed using the observed mappings.[2024-09-14 01:15:30.114] [jointLog] [info] Mapping rate = 100%[2024-09-14 01:15:30.114] [jointLog] [info] finished quantifyLibrary()[2024-09-14 01:15:30.118] [jointLog] [info] Starting optimizer[2024-09-14 01:15:30.119] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate[2024-09-14 01:15:30.119] [jointLog] [info] iteration = 0 | max rel diff. = 0[2024-09-14 01:15:30.120] [jointLog] [info] iteration = 100 | max rel diff. = 0[2024-09-14 01:15:30.120] [jointLog] [info] Finished optimizer[2024-09-14 01:15:30.120] [jointLog] [info] writing output [2024-09-14 01:15:30.125] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :Detected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details + ]]> + + + + + + + + 1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0contig count: 24 element count: 19592 complex nodes: 0# of ones in rank vector: 23[2024-09-14 01:15:57.437] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.[2024-09-14 01:15:57.437] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./indexsize = 19592-----------------------------------------| Loading contigs | Time = 1.3213 ms-----------------------------------------size = 19592-----------------------------------------| Loading contig boundaries | Time = 923.92 us-----------------------------------------Number of ones: 23Number of ones per inventory item: 512Inventory entries filled: 123[2024-09-14 01:15:57.440] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.[2024-09-14 01:15:57.440] [puff::index::jointLog] [info] contig count for validation: 23[2024-09-14 01:15:57.440] [puff::index::jointLog] [info] Total # of Contigs : 23[2024-09-14 01:15:57.440] [puff::index::jointLog] [info] Total # of numerical Contigs : 23[2024-09-14 01:15:57.441] [puff::index::jointLog] [info] Total # of contig vec entries: 36[2024-09-14 01:15:57.441] [puff::index::jointLog] [info] bits per offset entry 6[2024-09-14 01:15:57.441] [puff::index::jointLog] [info] Done constructing the contig vector. 24[2024-09-14 01:15:57.452] [puff::index::jointLog] [info] # segments = 23[2024-09-14 01:15:57.452] [puff::index::jointLog] [info] total length = 19592[2024-09-14 01:15:57.452] [puff::index::jointLog] 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BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[2024-09-14 01:15:57.548] [puff::index::jointLog] [info] mphf size = 0.0125198 MB[2024-09-14 01:15:57.548] [puff::index::jointLog] [info] chunk size = 9796[2024-09-14 01:15:57.548] [puff::index::jointLog] [info] chunk 0 = [0, 9796)[2024-09-14 01:15:57.548] [puff::index::jointLog] [info] chunk 1 = [9796, 19562)[2024-09-14 01:15:57.549] [puff::index::jointLog] [info] finished populating pos vector[2024-09-14 01:15:57.549] [puff::index::jointLog] [info] writing index components[2024-09-14 01:15:57.564] [puff::index::jointLog] [info] finished writing dense pufferfish index[2024-09-14 01:15:57.571] [jLog] [info] done building indexVersion Info: ### PLEASE UPGRADE SALMON ###### A newer version of salmon with important bug fixes and improvements is available. #######The newest version, available at https://github.com/COMBINE-lab/salmon/releasescontains new features, improvements, and bug fixes; please upgrade at yourearliest convenience.###Sign up for the salmon mailing list to hear about new versions, features and updates at:https://oceangenomics.com/subscribe###### salmon (selective-alignment-based) v1.3.0### [ program ] => salmon ### [ command ] => quant ### [ index ] => { ./index }### [ libType ] => { U }### [ unmatedReads ] => { ./single.fasta }### [ threads ] => { 6 }### [ seqBias ] => { }### [ gcBias ] => { }### [ incompatPrior ] => { 0.0 }### [ dumpEq ] => { }### [ minAssignedFrags ] => { 10 }### [ biasSpeedSamp ] => { 5 }### [ fldMax ] => { 1000 }### [ fldMean ] => { 250 }### [ fldSD ] => { 25 }### [ forgettingFactor ] => { 0.65 }### [ initUniform ] => { }### [ maxReadOcc ] => { 100 }### [ numBiasSamples ] => { 2000000 }### [ numAuxModelSamples ] => { 5000000 }### [ numPreAuxModelSamples ] => { 5000 }### [ useEM ] => { }### [ numGibbsSamples ] => { 0 }### [ noGammaDraw ] => { }### [ numBootstraps ] => { 0 }### [ thinningFactor ] => { 16 }### [ sigDigits ] => { 3 }### [ vbPrior ] => { 1e-05 }### [ output ] => { ./output }Logs will be written to ./output/logs[2024-09-14 01:15:57.655] [jointLog] [info] setting maxHashResizeThreads to 6[2024-09-14 01:15:57.655] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.[2024-09-14 01:15:57.655] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65[2024-09-14 01:15:57.655] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.[2024-09-14 01:15:57.655] [jointLog] [info] parsing read library format[2024-09-14 01:15:57.655] [jointLog] [info] There is 1 library.-----------------------------------------| Loading contig table | Time = 750.35 us-----------------------------------------size = 24-----------------------------------------| Loading contig offsets | Time = 1.2379 ms----------------------------------------------------------------------------------| Loading reference lengths | Time = 535.57 us----------------------------------------------------------------------------------| Loading mphf table | Time = 697.19 us-----------------------------------------size = 19592Number of ones: 23Number of ones per inventory item: 512Inventory entries filled: 1-----------------------------------------| Loading contig boundaries | Time = 986.83 us-----------------------------------------size = 19592-----------------------------------------| Loading sequence | Time = 845.78 us-----------------------------------------size = 18902-----------------------------------------| Loading positions | Time = 1.2133 ms-----------------------------------------size = 28562-----------------------------------------| Loading reference sequence | Time = 404.68 us----------------------------------------------------------------------------------| Loading reference accumulative lengths | Time = 368.4 us-----------------------------------------[2024-09-14 01:15:57.742] [jointLog] [info] Loading pufferfish index[2024-09-14 01:15:57.743] [jointLog] [info] Loading dense pufferfish index.[2024-09-14 01:15:57.752] [jointLog] [info] done[2024-09-14 01:15:57.752] [jointLog] [info] Index contained 15 targets[2024-09-14 01:15:57.753] [jointLog] [info] Number of decoys : 0[2024-09-14 01:15:57.753] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries. Please use this option with caution.[2024-09-14 01:15:57.800] [jointLog] [info] Computed 15 rich equivalence classes for further processing[2024-09-14 01:15:57.800] [jointLog] [info] Counted 15 total reads in the equivalence classes [2024-09-14 01:15:57.801] [jointLog] [info] Number of mappings discarded because of alignment score : 5[2024-09-14 01:15:57.801] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0[2024-09-14 01:15:57.801] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0[2024-09-14 01:15:57.801] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0[2024-09-14 01:15:57.801] [jointLog] [warning] Only 15 fragments were mapped, but the number of burn-in fragments was set to 5000000.The effective lengths have been computed using the observed mappings.[2024-09-14 01:15:57.801] [jointLog] [info] Mapping rate = 100%[2024-09-14 01:15:57.801] [jointLog] [info] finished quantifyLibrary()[2024-09-14 01:15:57.806] [jointLog] [info] Starting optimizer[2024-09-14 01:15:57.806] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate[2024-09-14 01:15:57.806] [jointLog] [info] iteration = 0 | max rel diff. = 49[2024-09-14 01:15:57.806] [jointLog] [info] iteration 3, adjusting effective lengths to account for biases[2024-09-14 01:15:57.811] [jointLog] [info] Computed expected counts (for bias correction)[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 20.0% of the transcripts[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 40.0% of the transcripts[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 46.7% of the transcripts[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 46.7% of the transcripts[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 46.7% of the transcripts[2024-09-14 01:15:57.812] [jointLog] [info] processed bias for 46.7% of the transcripts[2024-09-14 01:15:57.813] [jointLog] [info] processed bias for 53.3% of the transcripts[2024-09-14 01:15:57.813] [jointLog] [info] processed bias for 73.3% of the transcripts[2024-09-14 01:15:57.814] [jointLog] [info] processed bias for 100.0% of the transcripts[2024-09-14 01:15:57.814] [jointLog] [info] iteration = 100 | max rel diff. = 0[2024-09-14 01:15:57.814] [jointLog] [info] Finished optimizer[2024-09-14 01:15:57.814] [jointLog] [info] writing output [2024-09-14 01:15:57.819] [jointLog] [info] writing equivalence class counts.[2024-09-14 01:15:57.820] [jointLog] [info] Collapsing factorization information into simplified equivalence classes.[2024-09-14 01:15:57.820] [jointLog] [info] done.[2024-09-14 01:15:57.823] [jointLog] [info] done writing equivalence class counts.[2024-09-14 01:15:57.824] [jointLog] [warning] NOTE: Read Lib [[ ./single.fasta ]] :Detected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/tools.yml b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/tools.yml new file mode 100644 index 000000000..8b1c72bda --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-14-00-32-1/tools.yml @@ -0,0 +1,92 @@ +chunk: 10 +tools: +- name: annotatemyids + owner: iuc + revisions: + - 44018dd6b447 + tool_panel_section_label: Text Manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: datamash_reverse + owner: iuc + revisions: + - 0f1724dd59d2 + tool_panel_section_label: Datamash + tool_shed_url: toolshed.g2.bx.psu.edu +- name: trimmomatic + owner: pjbriggs + revisions: + - d94aff5ee623 + tool_panel_section_label: FASTQ Quality Control + tool_shed_url: toolshed.g2.bx.psu.edu +- name: samtools_fixmate + owner: iuc + revisions: + - bc0cc7bfbfe9 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: sam_to_bam + owner: devteam + revisions: + - cf1ffd88f895 + tool_panel_section_label: SAM/BAM + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bcftools_plugin_setgt + owner: iuc + revisions: + - 8abfcd1a6949 + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bcftools_call + owner: iuc + revisions: + - 072f606e2e69 + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcfbreakcreatemulti + owner: devteam + revisions: + - 9fd5d91eb91b + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: vcfselectsamples + owner: devteam + revisions: + - 2ba3b87f904f + tool_panel_section_label: VCF/BCF + tool_shed_url: toolshed.g2.bx.psu.edu +- name: poretools_occupancy + owner: iuc + revisions: + - 338d15b8d6fb + tool_panel_section_label: Nanopore + tool_shed_url: toolshed.g2.bx.psu.edu +- name: deeptools_plot_heatmap + owner: bgruening + revisions: + - a4dfb122e52b + tool_panel_section_label: deepTools + tool_shed_url: toolshed.g2.bx.psu.edu +- name: deeptools_plot_profile + owner: bgruening + revisions: + - c361b12d207a + tool_panel_section_label: deepTools + tool_shed_url: toolshed.g2.bx.psu.edu +- name: lofreq_filter + owner: iuc + revisions: + - 7dfca164d2e3 + tool_panel_section_label: Variant Calling + tool_shed_url: toolshed.g2.bx.psu.edu +- name: salmon + owner: bgruening + revisions: + - cc05793bb896 + tool_panel_section_label: RNA-seq + tool_shed_url: toolshed.g2.bx.psu.edu +- name: mummer_mummerplot + owner: iuc + revisions: + - ebe3b0f84de9 + tool_panel_section_label: Multiple Alignments + tool_shed_url: toolshed.g2.bx.psu.edu