From d6e16c6cc039140690ddc2cb693c811cc4e2c0d0 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Mon, 23 Sep 2024 14:16:34 +0000 Subject: [PATCH] Updating anvil-production README for prod-24-09-23-12-35-1 --- reports/anvil-production/README.md | 2 +- .../anvil-production/tool-tests/chunks.json | 10 +- .../prod-24-09-23-12-35-1/chunk.json | 7 + .../prod-24-09-23-12-35-1/chunk.txt | 15 + .../errors/0cad9bac291447c2.json | 44 + .../errors/2e416ed01d13ae5f.json | 48 + .../errors/6cdd2d16f3c221fc.json | 87 ++ .../errors/6d06355ae4d880d1.json | 47 + .../errors/7956cb04120de21b.json | 84 ++ .../errors/8c52fb4098cc199f.json | 48 + .../errors/9fa47fb7d0eeb78e.json | 44 + .../errors/b849e135bbda4f49.json | 98 ++ .../errors/d2fcdfe1ee2eaecf.json | 48 + .../prod-24-09-23-12-35-1/job-metrics.csv | 195 ++++ .../tool-tests/prod-24-09-23-12-35-1/jobs.txt | 194 ++++ .../paused/a06da25ef9238f7e.json | 59 + .../prod-24-09-23-12-35-1/results.html | 291 +++++ .../prod-24-09-23-12-35-1/results.json | 1 + .../prod-24-09-23-12-35-1/results.xunit | 1028 +++++++++++++++++ .../prod-24-09-23-12-35-1/tools.yml | 92 ++ 20 files changed, 2436 insertions(+), 6 deletions(-) create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/chunk.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/chunk.txt create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/0cad9bac291447c2.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/2e416ed01d13ae5f.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/6cdd2d16f3c221fc.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/6d06355ae4d880d1.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/7956cb04120de21b.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/8c52fb4098cc199f.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/9fa47fb7d0eeb78e.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/b849e135bbda4f49.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/d2fcdfe1ee2eaecf.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/job-metrics.csv create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/jobs.txt create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/paused/a06da25ef9238f7e.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/results.html create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/results.json create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/results.xunit create mode 100644 reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/tools.yml diff --git a/reports/anvil-production/README.md b/reports/anvil-production/README.md index dd112e2d9..7f62944b0 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 23 00:51:54 2024Mon Sep 16 00:51:53 2024
1ToolsetMon Sep 16 12:50:34 2024Mon Sep 09 12:50:13 2024
2ToolsetTue Sep 17 00:43:02 2024Tue Sep 10 00:48:20 2024
3ToolsetTue Sep 17 12:50:30 2024Tue Sep 10 12:51:55 2024
4ToolsetWed Sep 18 00:54:43 2024Wed Sep 04 00:47:35 2024
5ToolsetWed Sep 18 12:50:02 2024Wed Sep 11 12:50:17 2024
6ToolsetThu Sep 19 00:49:15 2024Thu Sep 12 00:49:13 2024
7ToolsetThu Sep 19 12:49:37 2024Thu Sep 12 12:49:05 2024
8ToolsetFri Sep 20 00:48:57 2024Fri Sep 13 00:47:48 2024
9ToolsetFri Sep 20 12:50:45 2024Fri Sep 13 12:48:35 2024
10ToolsetSat Sep 21 00:47:27 2024Sat Sep 14 00:47:35 2024
11ToolsetSat Sep 21 12:46:15 2024Sat Sep 14 12:48:11 2024
12ToolsetSun Sep 22 00:52:44 2024Sun Sep 15 00:52:44 2024
13ToolsetSun Sep 22 12:48:24 2024Sun Sep 15 12:47:00 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 23 00:51:54 2024Mon Sep 16 00:51:53 2024
1ToolsetMon Sep 23 12:51:18 2024Mon Sep 16 12:50:34 2024
2ToolsetTue Sep 17 00:43:02 2024Tue Sep 10 00:48:20 2024
3ToolsetTue Sep 17 12:50:30 2024Tue Sep 10 12:51:55 2024
4ToolsetWed Sep 18 00:54:43 2024Wed Sep 04 00:47:35 2024
5ToolsetWed Sep 18 12:50:02 2024Wed Sep 11 12:50:17 2024
6ToolsetThu Sep 19 00:49:15 2024Thu Sep 12 00:49:13 2024
7ToolsetThu Sep 19 12:49:37 2024Thu Sep 12 12:49:05 2024
8ToolsetFri Sep 20 00:48:57 2024Fri Sep 13 00:47:48 2024
9ToolsetFri Sep 20 12:50:45 2024Fri Sep 13 12:48:35 2024
10ToolsetSat Sep 21 00:47:27 2024Sat Sep 14 00:47:35 2024
11ToolsetSat Sep 21 12:46:15 2024Sat Sep 14 12:48:11 2024
12ToolsetSun Sep 22 00:52:44 2024Sun Sep 15 00:52:44 2024
13ToolsetSun Sep 22 12:48:24 2024Sun Sep 15 12:47:00 2024
diff --git a/reports/anvil-production/tool-tests/chunks.json b/reports/anvil-production/tool-tests/chunks.json index 9b8fb5f58..e03e3e116 100644 --- a/reports/anvil-production/tool-tests/chunks.json +++ b/reports/anvil-production/tool-tests/chunks.json @@ -35,11 +35,11 @@ "date2": "Tue Sep 10 12:51:55 2024" }, "1": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-16-12-35-1/results.html", - "date1": "Mon Sep 16 12:50:34 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-16-12-35-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-09-12-34-1/results.html", - "date2": "Mon Sep 09 12:50:13 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/results.html", + "date1": "Mon Sep 23 12:51:18 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-16-12-35-1/results.html", + "date2": "Mon Sep 16 12:50:34 2024" }, "2": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-17-00-27-1/results.html", diff --git a/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/chunk.json b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/chunk.json new file mode 100644 index 000000000..0f6eb565d --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/chunk.json @@ -0,0 +1,7 @@ +{ + "1": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/results.html", + "date1": "Mon Sep 23 12:51:18 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/chunk.txt b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/chunk.txt new file mode 100644 index 000000000..f18b9a19d --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/chunk.txt @@ -0,0 +1,15 @@ +-t ncbi_acc_download --tool-version 1c58de56d587 +-t add_input_name_as_column --tool-version 3284b72eef56 +-t fastq_groomer --tool-version 47e5dbc3e790 +-t samtools_reheader --tool-version 30388d878f81 +-t samtools_bedcov --tool-version 9149ad20699a +-t bedtools --tool-version ce3c7f062223 +-t bcftools_convert_from_vcf --tool-version b8e9da766b0f +-t bcftools_plugin_dosage --tool-version 5c232a738c74 +-t vcfflatten --tool-version f285aa6bdcfb +-t vcftools_slice --tool-version 1363e5d4a8b8 +-t poretools_winner --tool-version 79c1ac92f31b +-t deeptools_correct_gc_bias --tool-version 2c37ce318bc3 +-t bwameth --tool-version 29bdbc353f20 +-t snpeff --tool-version 74aebe30fb52 +-t edger --tool-version 334ce9b1bac5 diff --git a/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/0cad9bac291447c2.json b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/0cad9bac291447c2.json new file mode 100644 index 000000000..fb0ec5e61 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/0cad9bac291447c2.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "0cad9bac291447c2", + "state": "error", + "exit_code": null, + "update_time": "2024-09-23T13:18:57.146452", + "create_time": "2024-09-23T13:18:46.237518", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "947bb6702479ed20", + "external_id": "gxy-87ggd", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/99/registry.xml' '/galaxy/server/database/jobs_directory/000/99/upload_params.json' '118:/galaxy/server/database/objects/e/0/2/dataset_e0255e89-7a41-413a-bd53-ce83af0bc52d_files:/galaxy/server/database/objects/e/0/2/dataset_e0255e89-7a41-413a-bd53-ce83af0bc52d.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_14usucg5\"", + "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"eboVir3.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_9diqqwps\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"bam\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "c8764741bbb887fd", + "src": "hda", + "uuid": "e0255e89-7a41-413a-bd53-ce83af0bc52d" + } + }, + "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-24-09-23-12-35-1/errors/2e416ed01d13ae5f.json b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/2e416ed01d13ae5f.json new file mode 100644 index 000000000..23b2bacc3 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/2e416ed01d13ae5f.json @@ -0,0 +1,48 @@ +{ + "model_class": "Job", + "id": "2e416ed01d13ae5f", + "state": "error", + "exit_code": null, + "update_time": "2024-09-23T13:16:08.450429", + "create_time": "2024-09-23T13:16:03.315857", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", + "history_id": "947bb6702479ed20", + "external_id": "gxy-tmrhs", + "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/d/e/b/dataset_deb69f7d-fb95-4061-b65c-ff8c62fb783e.dat' cssanger.bz2 '/galaxy/server/database/objects/e/0/4/dataset_e043c9fc-efe8-4f74-a4af-b09713ad6881.dat' cssanger ascii summarize_input", + "traceback": null, + "params": { + "__input_ext": "\"fastq.bz2\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", + "input_type": "\"cssanger\"" + }, + "inputs": { + "input_file": { + "id": "00ceb129d5865519", + "src": "hda", + "uuid": "deb69f7d-fb95-4061-b65c-ff8c62fb783e" + } + }, + "outputs": { + "output_file": { + "id": "c7371e849dcb6dbd", + "src": "hda", + "uuid": "e043c9fc-efe8-4f74-a4af-b09713ad6881" + } + }, + "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-24-09-23-12-35-1/errors/6cdd2d16f3c221fc.json b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/6cdd2d16f3c221fc.json new file mode 100644 index 000000000..f6f872f29 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/6cdd2d16f3c221fc.json @@ -0,0 +1,87 @@ +{ + "model_class": "Job", + "id": "6cdd2d16f3c221fc", + "state": "error", + "exit_code": 0, + "update_time": "2024-09-23T13:26:40.642801", + "create_time": "2024-09-23T13:26:24.004271", + "galaxy_version": "23.1", + "command_version": "", + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1", + "history_id": "947bb6702479ed20", + "external_id": "gxy-ttmdk", + "command_line": "vcf-sort /galaxy/server/database/objects/e/7/2/dataset_e7207a25-878e-4480-940f-1479ba6dba90.dat > sorted.vcf ; echo '#dummy header' | cat - /galaxy/server/database/objects/f/9/a/dataset_f9a1fea0-a327-45fc-91c4-4cf8a6eb5057.dat > regions.bed ; vcftools --vcf sorted.vcf --out output --bed regions.bed --recode", + "traceback": null, + "params": { + "__input_ext": "\"vcf\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"" + }, + "inputs": { + "input": { + "id": "c16d38066b90b3b3", + "src": "hda", + "uuid": "e7207a25-878e-4480-940f-1479ba6dba90" + }, + "regions": { + "id": "d2c1b52b78bc35bb", + "src": "hda", + "uuid": "f9a1fea0-a327-45fc-91c4-4cf8a6eb5057" + } + }, + "outputs": { + "output": { + "id": "79679f468efbca13", + "src": "hda", + "uuid": "1fb6c01a-b1b9-487e-aaf9-25b611ba218e" + } + }, + "output_collections": {}, + "tool_stdout": "\nVCFtools - v0.1.11\n(C) Adam Auton 2009\n\nParameters as interpreted:\n\t--vcf sorted.vcf\n\t--out output\n\t--recode\n\t--bed regions.bed\n\nIndex file is older than variant file. Will regenerate.\nBuilding new index file.\nError:No header or meta information. Invalid file: sorted.vcf\n", + "tool_stderr": "/galaxy/server/database/jobs_directory/000/131/tool_script.sh: line 22: vcf-sort: command not found\n", + "job_stdout": "", + "job_stderr": "", + "stderr": "/galaxy/server/database/jobs_directory/000/131/tool_script.sh: line 22: vcf-sort: command not found\n", + "stdout": "\nVCFtools - v0.1.11\n(C) Adam Auton 2009\n\nParameters as interpreted:\n\t--vcf sorted.vcf\n\t--out output\n\t--recode\n\t--bed regions.bed\n\nIndex file is older than variant file. Will regenerate.\nBuilding new index file.\nError:No header or meta information. Invalid file: sorted.vcf\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": "2024-09-23 13:26:29", + "plugin": "core", + "name": "end_epoch", + "raw_value": "1727097989.0000000" + }, + { + "title": "Job Start Time", + "value": "2024-09-23 13:26:29", + "plugin": "core", + "name": "start_epoch", + "raw_value": "1727097989.0000000" + }, + { + "title": "Memory Allocated (MB)", + "value": "4080", + "plugin": "core", + "name": "galaxy_memory_mb", + "raw_value": "4080.0000000" + }, + { + "title": "Cores Allocated", + "value": "1", + "plugin": "core", + "name": "galaxy_slots", + "raw_value": "1.0000000" + } + ] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/6d06355ae4d880d1.json b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/6d06355ae4d880d1.json new file mode 100644 index 000000000..f55d353b0 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/6d06355ae4d880d1.json @@ -0,0 +1,47 @@ +{ + "model_class": "Job", + "id": "6d06355ae4d880d1", + "state": "error", + "exit_code": null, + "update_time": "2024-09-23T13:28:06.312944", + "create_time": "2024-09-23T13:28:00.206460", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_winner/poretools_winner/0.6.1a1.0", + "history_id": "947bb6702479ed20", + "external_id": "gxy-lts2x", + "command_line": "poretools winner --type all '/galaxy/server/database/objects/7/8/3/dataset_78345283-4682-41e9-9629-1805188c55a5.dat' > '/galaxy/server/database/objects/e/b/1/dataset_eb1b9008-bb7c-4b92-a15a-b93161671015.dat'", + "traceback": null, + "params": { + "__input_ext": "\"fast5.tar\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "type": "\"all\"" + }, + "inputs": { + "input": { + "id": "1ab519c4d5a3f600", + "src": "hda", + "uuid": "78345283-4682-41e9-9629-1805188c55a5" + } + }, + "outputs": { + "output": { + "id": "d0757380334e66c8", + "src": "hda", + "uuid": "eb1b9008-bb7c-4b92-a15a-b93161671015" + } + }, + "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-24-09-23-12-35-1/errors/7956cb04120de21b.json b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/7956cb04120de21b.json new file mode 100644 index 000000000..034b3642c --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/7956cb04120de21b.json @@ -0,0 +1,84 @@ +{ + "model_class": "Job", + "id": "7956cb04120de21b", + "state": "error", + "exit_code": 1, + "update_time": "2024-09-23T12:59:22.336268", + "create_time": "2024-09-23T12:59:09.755571", + "galaxy_version": "23.1", + "command_version": "", + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", + "history_id": "947bb6702479ed20", + "external_id": "gxy-4p88j", + "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/4/3/5/dataset_43579847-a887-42e8-bcfb-82cb86308b1c.dat' sanger '/galaxy/server/database/objects/4/f/8/dataset_4f883c4c-4e0e-439c-8b76-fe9918f340a6.dat' sanger ascii summarize_input --no-fix-id", + "traceback": null, + "params": { + "__input_ext": "\"fastq\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "options_type": "{\"__current_case__\": 1, \"fix_id\": false, \"force_quality_encoding\": \"ascii\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", + "input_type": "\"sanger\"" + }, + "inputs": { + "input_file": { + "id": "b39635dd5af16c5f", + "src": "hda", + "uuid": "43579847-a887-42e8-bcfb-82cb86308b1c" + } + }, + "outputs": { + "output_file": { + "id": "254170a0185eab4b", + "src": "hda", + "uuid": "4f883c4c-4e0e-439c-8b76-fe9918f340a6" + } + }, + "output_collections": {}, + "tool_stdout": "There was an error reading your input file. Your input file is likely malformed.\nIt is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below.\nHowever, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism.\n\nThe reported error is: 'Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).'.\nThe error occurred at the start of your file and no valid FASTQ reads were found.\nThe error in your file occurs between lines '1' and '3', which corresponds to byte-offsets '0' and '33', and contains the text (33 of 33 bytes shown):\n\n@FAKE-1\nACGTACGTAC\n+invalid line\n\n", + "tool_stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/gx-fastq-groomer\", line 10, in \n sys.exit(main())\n ^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 99, in main\n Groomer().run()\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 48, in run\n for read_count, fastq_read in enumerate(reader):\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 683, in __iter__\n yield next(self)\n ^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 742, in __next__\n raise e\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 724, in __next__\n block = super(fastqVerboseErrorReader, self).__next__()\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 621, in __next__\n self._read_fastq_sequence(rval, id_line)\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 666, in _read_fastq_sequence\n raise fastqFormatError(\ngalaxy_utils.sequence.fastq.fastqFormatError: Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).\n", + "job_stdout": "", + "job_stderr": "", + "stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/gx-fastq-groomer\", line 10, in \n sys.exit(main())\n ^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 99, in main\n Groomer().run()\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 48, in run\n for read_count, fastq_read in enumerate(reader):\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 683, in __iter__\n yield next(self)\n ^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 742, in __next__\n raise e\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 724, in __next__\n block = super(fastqVerboseErrorReader, self).__next__()\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 621, in __next__\n self._read_fastq_sequence(rval, id_line)\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 666, in _read_fastq_sequence\n raise fastqFormatError(\ngalaxy_utils.sequence.fastq.fastqFormatError: Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).\n", + "stdout": "There was an error reading your input file. Your input file is likely malformed.\nIt is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below.\nHowever, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism.\n\nThe reported error is: 'Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).'.\nThe error occurred at the start of your file and no valid FASTQ reads were found.\nThe error in your file occurs between lines '1' and '3', which corresponds to byte-offsets '0' and '33', and contains the text (33 of 33 bytes shown):\n\n@FAKE-1\nACGTACGTAC\n+invalid line\n\n", + "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": "2024-09-23 12:59:11", + "plugin": "core", + "name": "end_epoch", + "raw_value": "1727096351.0000000" + }, + { + "title": "Job Start Time", + "value": "2024-09-23 12:59:11", + "plugin": "core", + "name": "start_epoch", + "raw_value": "1727096351.0000000" + }, + { + "title": "Memory Allocated (MB)", + "value": "8160", + "plugin": "core", + "name": "galaxy_memory_mb", + "raw_value": "8160.0000000" + }, + { + "title": "Cores Allocated", + "value": "1", + "plugin": "core", + "name": "galaxy_slots", + "raw_value": "1.0000000" + } + ] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/8c52fb4098cc199f.json b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/8c52fb4098cc199f.json new file mode 100644 index 000000000..b4f399b2d --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/8c52fb4098cc199f.json @@ -0,0 +1,48 @@ +{ + "model_class": "Job", + "id": "8c52fb4098cc199f", + "state": "error", + "exit_code": null, + "update_time": "2024-09-23T13:30:44.908573", + "create_time": "2024-09-23T13:30:39.855461", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "CONVERTER_gz_to_uncompressed", + "history_id": "947bb6702479ed20", + "external_id": "gxy-g8ln2", + "command_line": "cp '/galaxy/server/database/jobs_directory/000/147/configs/tmpiq7bsrvc' 'galaxy.json' && gzip -dcf '/galaxy/server/database/objects/a/4/1/dataset_a41e95a1-c950-45b7-b100-5c002cbb285e.dat' > '/galaxy/server/database/objects/1/f/b/dataset_1fb8e9d9-ea79-42f3-b81a-8a936e04c841.dat'", + "traceback": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "__target_datatype__": "\"fasta\"", + "__current_case__": "0" + }, + "inputs": { + "input1": { + "id": "f8c781446a345c70", + "src": "hda", + "uuid": "a41e95a1-c950-45b7-b100-5c002cbb285e" + } + }, + "outputs": { + "output1": { + "id": "d7578f35ab2a3690", + "src": "hda", + "uuid": "1fb8e9d9-ea79-42f3-b81a-8a936e04c841" + } + }, + "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-24-09-23-12-35-1/errors/9fa47fb7d0eeb78e.json b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/9fa47fb7d0eeb78e.json new file mode 100644 index 000000000..17761e21c --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/9fa47fb7d0eeb78e.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "9fa47fb7d0eeb78e", + "state": "error", + "exit_code": null, + "update_time": "2024-09-23T13:03:56.874860", + "create_time": "2024-09-23T13:03:45.858059", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "947bb6702479ed20", + "external_id": "gxy-z24gz", + "command_line": "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' '57:/galaxy/server/database/objects/4/6/6/dataset_46629445-2ec0-4d5f-ad48-6076ff49d710_files:/galaxy/server/database/objects/4/6/6/dataset_46629445-2ec0-4d5f-ad48-6076ff49d710.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_2iyd9is6\"", + "files_metadata": "{\"__current_case__\": 78, \"file_type\": \"fastq\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"illumina_full_range_original_illumina.fastqillumina\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_1ao5j5wc\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastq\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "7c4d957c0fc535c5", + "src": "hda", + "uuid": "46629445-2ec0-4d5f-ad48-6076ff49d710" + } + }, + "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-24-09-23-12-35-1/errors/b849e135bbda4f49.json b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/b849e135bbda4f49.json new file mode 100644 index 000000000..7c81bb153 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/b849e135bbda4f49.json @@ -0,0 +1,98 @@ +{ + "model_class": "Job", + "id": "b849e135bbda4f49", + "state": "error", + "exit_code": 1, + "update_time": "2024-09-23T12:56:45.836057", + "create_time": "2024-09-23T12:56:29.932232", + "galaxy_version": "23.1", + "command_version": "", + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0", + "history_id": "947bb6702479ed20", + "external_id": "gxy-ps29p", + "command_line": "echo 'CP011064,CP0XXXXX,CP021680' | sed -r 's/(\\,|__cn__)/\\n/g' | grep -v \"^[ \\t]*$\" > accessions && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'fasta' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", + "traceback": null, + "params": { + "__input_ext": "\"data\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "ignore_failed": "\"0\"", + "range": null, + "molecule": "{\"__current_case__\": 0, \"format\": \"fasta\", \"select\": \"nucleotide\"}", + "query_source": "{\"__current_case__\": 1, \"accession_list\": \"CP011064,CP0XXXXX,CP021680\", \"select\": \"accession_list\"}" + }, + "inputs": {}, + "outputs": { + "error_log": { + "id": "4cfff3c5fffdf472", + "src": "hda", + "uuid": "da145c5a-473f-4027-b1a1-0a5d32c1d54a" + }, + "__new_primary_file_output|CP011064__": { + "id": "18f54c2e60adeca1", + "src": "hda", + "uuid": "344cc865-aa34-4b7d-a330-8afc1f3d1d43" + } + }, + "output_collections": { + "output": { + "id": "dc350d755d4846e0", + "src": "hdca" + } + }, + "tool_stdout": "NCBI Entrez returned error code 400, are ID(s) CP0XXXXX valid?\n", + "tool_stderr": "Failed to download file with id CP0XXXXX from NCBI\n", + "job_stdout": "", + "job_stderr": "", + "stderr": "Failed to download file with id CP0XXXXX from NCBI\n", + "stdout": "NCBI Entrez returned error code 400, are ID(s) CP0XXXXX valid?\n", + "job_messages": [ + { + "code_desc": "", + "desc": "Fatal error: Exit code 1 ()", + "error_level": 3, + "exit_code": 1, + "type": "exit_code" + } + ], + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [ + { + "title": "Job Runtime (Wall Clock)", + "value": "4 seconds", + "plugin": "core", + "name": "runtime_seconds", + "raw_value": "4.0000000" + }, + { + "title": "Job End Time", + "value": "2024-09-23 12:56:36", + "plugin": "core", + "name": "end_epoch", + "raw_value": "1727096196.0000000" + }, + { + "title": "Job Start Time", + "value": "2024-09-23 12:56:32", + "plugin": "core", + "name": "start_epoch", + "raw_value": "1727096192.0000000" + }, + { + "title": "Memory Allocated (MB)", + "value": "4080", + "plugin": "core", + "name": "galaxy_memory_mb", + "raw_value": "4080.0000000" + }, + { + "title": "Cores Allocated", + "value": "1", + "plugin": "core", + "name": "galaxy_slots", + "raw_value": "1.0000000" + } + ] +} diff --git a/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/d2fcdfe1ee2eaecf.json b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/d2fcdfe1ee2eaecf.json new file mode 100644 index 000000000..07af1c443 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/errors/d2fcdfe1ee2eaecf.json @@ -0,0 +1,48 @@ +{ + "model_class": "Job", + "id": "d2fcdfe1ee2eaecf", + "state": "error", + "exit_code": null, + "update_time": "2024-09-23T13:05:26.032819", + "create_time": "2024-09-23T13:05:20.045345", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", + "history_id": "947bb6702479ed20", + "external_id": "gxy-qxwjx", + "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/2/1/9/dataset_219116cc-64df-4cbc-a2f3-2d2d4bb448c1.dat' sanger '/galaxy/server/database/objects/0/c/5/dataset_0c5f4c97-d6fa-4586-80e7-e13e70528905.dat' solexa None summarize_input --fix-id", + "traceback": null, + "params": { + "__input_ext": "\"fastq\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"solexa\", \"summarize_input\": \"summarize_input\"}", + "input_type": "\"sanger\"" + }, + "inputs": { + "input_file": { + "id": "79476c07c539c4c6", + "src": "hda", + "uuid": "219116cc-64df-4cbc-a2f3-2d2d4bb448c1" + } + }, + "outputs": { + "output_file": { + "id": "cffcc2f915fa8f8e", + "src": "hda", + "uuid": "0c5f4c97-d6fa-4586-80e7-e13e70528905" + } + }, + "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-24-09-23-12-35-1/job-metrics.csv b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/job-metrics.csv new file mode 100644 index 000000000..4ace2c5b6 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/job-metrics.csv @@ -0,0 +1,195 @@ +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 +d9fa21207a1992e9,947bb6702479ed20,anvil-test-2024-09-23-12-51,ok,edger/3.36.0+galaxy5,,,,20401.0000000,1.0000000,,,,,,6.0000000 +4af7ffcdd450b0de,947bb6702479ed20,anvil-test-2024-09-23-12-51,ok,upload1,,,,4080.0000000,1.0000000,,,,,,6.0000000 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2024-09-23T13:23:12.163523 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4 +7d2e563e44054c8d ok 2024-09-23T13:22:59.383016 upload1 +52df11bc3beb3f0f ok 2024-09-23T13:22:40.172574 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4 +346ceefe90120c58 ok 2024-09-23T13:22:25.865050 upload1 +4ead75f5169732de ok 2024-09-23T13:22:05.714826 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4 +b9ffb27a70ba8f85 ok 2024-09-23T13:21:47.311531 upload1 +76be110c0ab4b2ff ok 2024-09-23T13:21:26.271386 toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4 +0038c31cd63c8e1a ok 2024-09-23T13:21:11.970826 upload1 +37d91fcf4fac7e52 ok 2024-09-23T13:21:10.307487 upload1 +24bf176a33c16aaf ok 2024-09-23T13:20:50.646272 toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.4 +5696cc386921e2ac ok 2024-09-23T13:20:35.841234 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toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +78c81aba8ba91511 ok 2024-09-23T13:15:29.495702 upload1 +a650938ff37ae699 ok 2024-09-23T13:15:09.221289 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +0c6443eeb7a0fc27 ok 2024-09-23T13:14:55.130726 upload1 +e5c6fd44d073f013 ok 2024-09-23T13:14:35.894170 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +bf07d796a754091e ok 2024-09-23T13:14:23.489842 upload1 +c12415ed4ebe13a5 ok 2024-09-23T13:14:05.471794 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +c8562924fdbcf149 ok 2024-09-23T13:13:51.235126 upload1 +076271d24313dd49 ok 2024-09-23T13:13:31.765673 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +c37d3bcc697e9df0 ok 2024-09-23T13:13:17.901024 upload1 +9642d6f68834efd5 ok 2024-09-23T13:12:57.575899 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +bd18c3786bd9c47a ok 2024-09-23T13:12:45.267307 upload1 +1e862f876c47a0da ok 2024-09-23T13:12:27.073952 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +f51da42d371d039e ok 2024-09-23T13:12:12.805156 upload1 +9f26fccc1bbfb9c4 ok 2024-09-23T13:11:52.485691 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +57067365a9ea695e ok 2024-09-23T13:11:38.409019 upload1 +6d0f65f4e5c34f24 ok 2024-09-23T13:11:20.209517 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +48009a930b8487fd ok 2024-09-23T13:11:07.007765 upload1 +dfa41e1c924687cb ok 2024-09-23T13:10:48.796934 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +cffcc2f915fa8f8e ok 2024-09-23T13:10:35.695267 upload1 +79476c07c539c4c6 ok 2024-09-23T13:10:16.521754 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +496c9883c2047cac ok 2024-09-23T13:10:02.119557 upload1 +5fc5874de7554e71 ok 2024-09-23T13:09:43.860047 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +347acdfe43aed5cd ok 2024-09-23T13:09:30.904226 upload1 +f78423128d8952ce ok 2024-09-23T13:09:12.434273 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +7c4d957c0fc535c5 ok 2024-09-23T13:08:59.448354 upload1 +74e9734e5ab1e351 ok 2024-09-23T13:08:40.267328 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +6b642e1d74c8bf61 ok 2024-09-23T13:08:26.254779 upload1 +9e9bef3212786702 ok 2024-09-23T13:08:07.033874 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +e609d34f51e3c720 ok 2024-09-23T13:07:53.625203 upload1 +8dfb5501d2079009 ok 2024-09-23T13:07:33.164145 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +8968cffb028e4eba ok 2024-09-23T13:07:21.130075 upload1 +374937641cb6242d ok 2024-09-23T13:07:01.855388 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +af045946503fce90 ok 2024-09-23T13:06:49.872910 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toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +d33c8b981e3be902 ok 2024-09-23T13:03:30.052919 upload1 +7956f1cdb5e2e625 ok 2024-09-23T13:03:09.732703 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +5fc883da7dbbb2f2 ok 2024-09-23T13:02:56.517978 upload1 +13677f2b12ecd8d8 ok 2024-09-23T13:02:37.257039 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +3746860e8acbb4f1 ok 2024-09-23T13:02:23.908053 upload1 +431d179f1c8481cc ok 2024-09-23T13:02:05.743260 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +21275dc69ec9a814 ok 2024-09-23T13:01:52.431506 upload1 +d1e4507abeaf9074 ok 2024-09-23T13:01:33.187773 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +3519a27c8a4c06b6 ok 2024-09-23T13:01:20.335221 upload1 +18f54c2e60adeca1 ok 2024-09-23T13:01:00.751529 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +4cfff3c5fffdf472 ok 2024-09-23T13:00:47.625937 upload1 +09edacbd04fc16f4 ok 2024-09-23T13:00:27.585878 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +aea23146ae2f4d21 ok 2024-09-23T13:00:14.137085 upload1 +df3c8fdfb989b284 ok 2024-09-23T12:59:54.865273 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +ac4b0d61c0d502ff ok 2024-09-23T12:59:41.673321 upload1 +7956cb04120de21b error 2024-09-23T12:59:22.336268 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +748026805d8e73fb ok 2024-09-23T12:59:09.403913 upload1 +bf2816cafd88ee85 ok 2024-09-23T12:58:50.794270 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +d541feba2561bfc4 ok 2024-09-23T12:58:36.734946 upload1 +0d2adb38b7fe86ec ok 2024-09-23T12:58:17.494536 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 +4675913052c074b4 ok 2024-09-23T12:57:58.891281 upload1 +327271a847b6aeda ok 2024-09-23T12:57:36.406580 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +f2aa66eb32c75d54 ok 2024-09-23T12:57:20.410395 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +0f809caf69144a2f ok 2024-09-23T12:57:03.948103 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +b849e135bbda4f49 error 2024-09-23T12:56:45.836057 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +b4ffb4ffa6e15902 ok 2024-09-23T12:56:28.653330 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +09e002d77c54e484 ok 2024-09-23T12:56:12.386180 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +0ebe743b0a6a67ba ok 2024-09-23T12:55:50.101125 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +dc350d755d4846e0 ok 2024-09-23T12:55:29.731549 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +fa37247bbcc1ec5a ok 2024-09-23T12:55:11.370171 upload1 +2079e80a52b9f098 ok 2024-09-23T12:54:50.998464 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +ca1a7ff542832f6a ok 2024-09-23T12:54:31.560887 upload1 +4b0485460146f85a ok 2024-09-23T12:54:12.422008 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +72098edaf93336c2 ok 2024-09-23T12:53:53.960718 upload1 +2de01d98ed94e7fa ok 2024-09-23T12:53:35.079619 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +947bb6702479ed20 ok 2024-09-23T12:52:43.631296 upload1 diff --git a/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/paused/a06da25ef9238f7e.json b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/paused/a06da25ef9238f7e.json new file mode 100644 index 000000000..4329c4fca --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/paused/a06da25ef9238f7e.json @@ -0,0 +1,59 @@ +{ + "model_class": "Job", + "id": "a06da25ef9238f7e", + "state": "paused", + "exit_code": null, + "update_time": "2024-09-23T13:30:44.909844", + "create_time": "2024-09-23T13:30:39.976109", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0", + "history_id": "947bb6702479ed20", + "external_id": null, + "command_line": null, + "traceback": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "readGroup": "\"\"", + "single_or_paired": "{\"__current_case__\": 1, \"input_mate1\": {\"values\": [{\"id\": 173, \"src\": \"hda\"}]}, \"input_mate2\": {\"values\": [{\"id\": 174, \"src\": \"hda\"}]}, \"single_or_paired_opts\": \"paired\"}", + "referenceSource": "{\"__current_case__\": 0, \"reference\": {\"values\": [{\"id\": 175, \"src\": \"hda\"}]}, \"source\": \"history\"}" + }, + "inputs": { + "referenceSource|reference": { + "id": "d7578f35ab2a3690", + "src": "hda", + "uuid": "1fb8e9d9-ea79-42f3-b81a-8a936e04c841" + }, + "single_or_paired|input_mate1": { + "id": "2dd39c81427ee5bd", + "src": "hda", + "uuid": "2a831fd0-5c5e-4955-959e-94ef14b88e8e" + }, + "single_or_paired|input_mate2": { + "id": "05ccd5f464c64737", + "src": "hda", + "uuid": "330fc1a1-b134-4abd-9113-a87587200e01" + } + }, + "outputs": { + "output": { + "id": "fb7603d2b2400d35", + "src": "hda", + "uuid": "5737af86-0013-432e-8f21-7b8744093a6b" + } + }, + "output_collections": {}, + "tool_stdout": null, + "tool_stderr": null, + "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-24-09-23-12-35-1/results.html b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/results.html new file mode 100644 index 000000000..0daa6278e --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/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-24-09-23-12-35-1/results.json b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/results.json new file mode 100644 index 000000000..496b94299 --- /dev/null +++ b/reports/anvil-production/tool-tests/prod-24-09-23-12-35-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 84, "errors": 2, "failures": 5, "skips": 0}, "tests": [{"id": "bcftools_convert_from_vcf/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_convert_from_vcf", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 37.76678204536438, "inputs": {"input_file": {"src": "hda", "id": "35d54094276bc7ae"}, "convert|convert_to": "gen_sample"}, "job": {"model_class": "Job", "id": "4ead75f5169732de", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:22:05.714826", "create_time": "2024-09-23T13:21:47.913909", "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_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4", "history_id": "947bb6702479ed20", "external_id": "gxy-8hzfk", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/1/f/8/dataset_1f81641c-03a8-4ed9-a99a-713deb553ff2.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools convert --tag GT --gensample \"/galaxy/server/database/objects/a/c/c/dataset_acc968ab-7ee6-4c6d-842d-34edc6d92269.dat,/galaxy/server/database/objects/2/c/5/dataset_2c5397fb-6c8e-425b-839f-d6efe01fe2c6.dat\" \"/galaxy/server/database/objects/1/f/8/dataset_1f81641c-03a8-4ed9-a99a-713deb553ff2.dat\" .", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "convert": "{\"__current_case__\": 0, \"convert_3N6\": false, \"convert_to\": \"gen_sample\", \"sex_info\": {\"__current_case__\": 0, \"sex_info_src\": \"none\"}, \"tag\": \"GT\", \"vcf_ids\": false}", "keep_duplicates": "false", "sec_restrict": "{\"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "35d54094276bc7ae", "src": "hda", "uuid": "1f81641c-03a8-4ed9-a99a-713deb553ff2"}}, "outputs": {"output_gen": {"id": "c5816eb39254e694", "src": "hda", "uuid": "acc968ab-7ee6-4c6d-842d-34edc6d92269"}, "output_samples": {"id": "3ae64922413031d5", "src": "hda", "uuid": "2c5397fb-6c8e-425b-839f-d6efe01fe2c6"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Gen file: /galaxy/server/database/objects/a/c/c/dataset_acc968ab-7ee6-4c6d-842d-34edc6d92269.dat\nSample file: /galaxy/server/database/objects/2/c/5/dataset_2c5397fb-6c8e-425b-839f-d6efe01fe2c6.dat\nWarning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n32 records written, 1 skipped: 0/1/0/0 no-ALT/non-biallelic/filtered/duplicated\n", "job_stdout": "", "job_stderr": "", "stderr": "Gen file: /galaxy/server/database/objects/a/c/c/dataset_acc968ab-7ee6-4c6d-842d-34edc6d92269.dat\nSample file: /galaxy/server/database/objects/2/c/5/dataset_2c5397fb-6c8e-425b-839f-d6efe01fe2c6.dat\nWarning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n32 records written, 1 skipped: 0/1/0/0 no-ALT/non-biallelic/filtered/duplicated\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": "2024-09-23 13:21:54", "plugin": "core", "name": "end_epoch", "raw_value": "1727097714.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:21:53", "plugin": "core", "name": "start_epoch", "raw_value": "1727097713.0000000"}, {"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_convert_from_vcf/1.15.1+galaxy4-1", "has_data": true, "data": {"tool_id": "bcftools_convert_from_vcf", "tool_version": "1.15.1+galaxy4", "test_index": 1, "time_seconds": 33.579988956451416, "inputs": {"input_file": {"src": "hda", "id": "6d06355ae4d880d1"}, "convert|tag": "GP", "convert|convert_3N6": true, "convert|convert_to": "gen_sample"}, "job": {"model_class": "Job", "id": "52df11bc3beb3f0f", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:22:40.172574", "create_time": "2024-09-23T13:22:26.167078", "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_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4", "history_id": "947bb6702479ed20", "external_id": "gxy-x99gn", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/d/c/dataset_fdca6bee-f5a2-4143-8b07-8a79d6fc8cac.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools convert --tag GP --3N6 --gensample \"/galaxy/server/database/objects/4/e/2/dataset_4e2de65b-5d0e-4eb4-bef5-1689e7ef16c7.dat,/galaxy/server/database/objects/0/c/1/dataset_0c1c4403-9ab8-45fb-ba8d-1ca194d1ed50.dat\" \"/galaxy/server/database/objects/f/d/c/dataset_fdca6bee-f5a2-4143-8b07-8a79d6fc8cac.dat\" .", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "convert": "{\"__current_case__\": 0, \"convert_3N6\": true, \"convert_to\": \"gen_sample\", \"sex_info\": {\"__current_case__\": 0, \"sex_info_src\": \"none\"}, \"tag\": \"GP\", \"vcf_ids\": false}", "keep_duplicates": "false", "sec_restrict": "{\"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "6d06355ae4d880d1", "src": "hda", "uuid": "fdca6bee-f5a2-4143-8b07-8a79d6fc8cac"}}, "outputs": {"output_gen": {"id": "e6aa888b8e4bb665", "src": "hda", "uuid": "4e2de65b-5d0e-4eb4-bef5-1689e7ef16c7"}, "output_samples": {"id": "4eb96695f22946fe", "src": "hda", "uuid": "0c1c4403-9ab8-45fb-ba8d-1ca194d1ed50"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Gen file: /galaxy/server/database/objects/4/e/2/dataset_4e2de65b-5d0e-4eb4-bef5-1689e7ef16c7.dat\nSample file: /galaxy/server/database/objects/0/c/1/dataset_0c1c4403-9ab8-45fb-ba8d-1ca194d1ed50.dat\nWarning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n32 records written, 1 skipped: 0/1/0/0 no-ALT/non-biallelic/filtered/duplicated\n", "job_stdout": "", "job_stderr": "", "stderr": "Gen file: /galaxy/server/database/objects/4/e/2/dataset_4e2de65b-5d0e-4eb4-bef5-1689e7ef16c7.dat\nSample file: /galaxy/server/database/objects/0/c/1/dataset_0c1c4403-9ab8-45fb-ba8d-1ca194d1ed50.dat\nWarning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n32 records written, 1 skipped: 0/1/0/0 no-ALT/non-biallelic/filtered/duplicated\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": "2024-09-23 13:22:28", "plugin": "core", "name": "end_epoch", "raw_value": "1727097748.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:22:28", "plugin": "core", "name": "start_epoch", "raw_value": "1727097748.0000000"}, {"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_convert_from_vcf/1.15.1+galaxy4-2", "has_data": true, "data": {"tool_id": "bcftools_convert_from_vcf", "tool_version": "1.15.1+galaxy4", "test_index": 2, "time_seconds": 31.802645921707153, "inputs": {"input_file": {"src": "hda", "id": "0639ac05e3644dfa"}, "convert|tag": "GT", "convert|convert_3N6": true, "convert|vcf_ids": true, "convert|convert_to": "gen_sample"}, "job": {"model_class": "Job", "id": "c8764741bbb887fd", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:23:12.163523", "create_time": "2024-09-23T13:22:59.834100", "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_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4", "history_id": "947bb6702479ed20", "external_id": "gxy-z7jkd", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/4/9/3/dataset_493d153f-03ef-48b2-9274-d23cf3a7fc82.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools convert --tag GT --3N6 --vcf-ids --gensample \"/galaxy/server/database/objects/5/7/1/dataset_5715ddba-92fe-4539-9d78-2a8a0b8b57d1.dat,/galaxy/server/database/objects/4/7/6/dataset_4765dcaf-ddb5-486e-ba5e-30f3dd559c13.dat\" \"/galaxy/server/database/objects/4/9/3/dataset_493d153f-03ef-48b2-9274-d23cf3a7fc82.dat\" .", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "convert": "{\"__current_case__\": 0, \"convert_3N6\": true, \"convert_to\": \"gen_sample\", \"sex_info\": {\"__current_case__\": 0, \"sex_info_src\": \"none\"}, \"tag\": \"GT\", \"vcf_ids\": true}", "keep_duplicates": "false", "sec_restrict": "{\"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "0639ac05e3644dfa", "src": "hda", "uuid": "493d153f-03ef-48b2-9274-d23cf3a7fc82"}}, "outputs": {"output_gen": {"id": "e0c4a8e0a9995d3a", "src": "hda", "uuid": "5715ddba-92fe-4539-9d78-2a8a0b8b57d1"}, "output_samples": {"id": "936bb6dad48bd237", "src": "hda", "uuid": "4765dcaf-ddb5-486e-ba5e-30f3dd559c13"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Gen file: /galaxy/server/database/objects/5/7/1/dataset_5715ddba-92fe-4539-9d78-2a8a0b8b57d1.dat\nSample file: /galaxy/server/database/objects/4/7/6/dataset_4765dcaf-ddb5-486e-ba5e-30f3dd559c13.dat\nWarning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n[W::vcf_parse] Contig '2' is not defined in the header. (Quick workaround: index the file with tabix.)\n10 records written, 8 skipped: 0/6/0/2 no-ALT/non-biallelic/filtered/duplicated\n", "job_stdout": "", "job_stderr": "", "stderr": "Gen file: /galaxy/server/database/objects/5/7/1/dataset_5715ddba-92fe-4539-9d78-2a8a0b8b57d1.dat\nSample file: /galaxy/server/database/objects/4/7/6/dataset_4765dcaf-ddb5-486e-ba5e-30f3dd559c13.dat\nWarning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n[W::vcf_parse] Contig '2' is not defined in the header. (Quick workaround: index the file with tabix.)\n10 records written, 8 skipped: 0/6/0/2 no-ALT/non-biallelic/filtered/duplicated\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": "2024-09-23 13:23:02", "plugin": "core", "name": "end_epoch", "raw_value": "1727097782.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:23:01", "plugin": "core", "name": "start_epoch", "raw_value": "1727097781.0000000"}, {"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_convert_from_vcf/1.15.1+galaxy4-3", "has_data": true, "data": {"tool_id": "bcftools_convert_from_vcf", "tool_version": "1.15.1+galaxy4", "test_index": 3, "time_seconds": 33.53737282752991, "inputs": {"input_file": {"src": "hda", "id": "af695465274f3da1"}, "convert|convert_to": "hap_sample"}, "job": {"model_class": "Job", "id": "7886515453650081", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:23:45.832027", "create_time": "2024-09-23T13:23:31.834756", "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_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4", "history_id": "947bb6702479ed20", "external_id": "gxy-jdqjl", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/d/7/9/dataset_d79597d5-3eb7-48ea-81b6-899cdde43791.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools convert --hapsample \"/galaxy/server/database/objects/f/7/8/dataset_f78ba0e0-0606-4342-8a3b-3f3989d2e17c.dat,/galaxy/server/database/objects/5/d/9/dataset_5d9407eb-106d-49d0-bd63-463ed50aef3b.dat\" \"/galaxy/server/database/objects/d/7/9/dataset_d79597d5-3eb7-48ea-81b6-899cdde43791.dat\" .", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "convert": "{\"__current_case__\": 1, \"convert_to\": \"hap_sample\", \"haploid2diploid\": false, \"sex_info\": {\"__current_case__\": 0, \"sex_info_src\": \"none\"}, \"vcf_ids\": false}", "keep_duplicates": "false", "sec_restrict": "{\"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "af695465274f3da1", "src": "hda", "uuid": "d79597d5-3eb7-48ea-81b6-899cdde43791"}}, "outputs": {"output_hap": {"id": "5cb98b0d1c876ce5", "src": "hda", "uuid": "f78ba0e0-0606-4342-8a3b-3f3989d2e17c"}, "output_samples": {"id": "9cdc6b8f809b4df7", "src": "hda", "uuid": "5d9407eb-106d-49d0-bd63-463ed50aef3b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Hap file: /galaxy/server/database/objects/f/7/8/dataset_f78ba0e0-0606-4342-8a3b-3f3989d2e17c.dat\nSample file: /galaxy/server/database/objects/5/d/9/dataset_5d9407eb-106d-49d0-bd63-463ed50aef3b.dat\nWarning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n32 records written, 1 skipped: 0/1/0 no-ALT/non-biallelic/filtered\n", "job_stdout": "", "job_stderr": "", "stderr": "Hap file: /galaxy/server/database/objects/f/7/8/dataset_f78ba0e0-0606-4342-8a3b-3f3989d2e17c.dat\nSample file: /galaxy/server/database/objects/5/d/9/dataset_5d9407eb-106d-49d0-bd63-463ed50aef3b.dat\nWarning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n32 records written, 1 skipped: 0/1/0 no-ALT/non-biallelic/filtered\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": "2024-09-23 13:23:34", "plugin": "core", "name": "end_epoch", "raw_value": "1727097814.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:23:33", "plugin": "core", "name": "start_epoch", "raw_value": "1727097813.0000000"}, {"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_convert_from_vcf/1.15.1+galaxy4-4", "has_data": true, "data": {"tool_id": "bcftools_convert_from_vcf", "tool_version": "1.15.1+galaxy4", "test_index": 4, "time_seconds": 32.805779218673706, "inputs": {"input_file": {"src": "hda", "id": "ed4992a79ef4e676"}, "convert|convert_to": "hap_legend_sample"}, "job": {"model_class": "Job", "id": "edff6a4e438e2455", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:24:17.331829", "create_time": "2024-09-23T13:24:04.267332", "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_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4", "history_id": "947bb6702479ed20", "external_id": "gxy-5ckrr", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/0/7/9/dataset_07918ab5-608d-485b-9064-b0f205240be4.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools convert --haplegendsample \"/galaxy/server/database/objects/4/5/f/dataset_45ff78c2-c0b4-4633-9ee0-13ffeacb3c5d.dat,/galaxy/server/database/objects/b/a/0/dataset_ba076ec3-fb09-48e7-adb8-38d9945ada03.dat,/galaxy/server/database/objects/d/9/c/dataset_d9c6b2b6-182e-4e8b-b051-40534e36c16a.dat\" \"/galaxy/server/database/objects/0/7/9/dataset_07918ab5-608d-485b-9064-b0f205240be4.dat\" .", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "convert": "{\"__current_case__\": 2, \"convert_to\": \"hap_legend_sample\", \"haploid2diploid\": false, \"sex_info\": {\"__current_case__\": 0, \"sex_info_src\": \"none\"}, \"vcf_ids\": false}", "keep_duplicates": "false", "sec_restrict": "{\"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "ed4992a79ef4e676", "src": "hda", "uuid": "07918ab5-608d-485b-9064-b0f205240be4"}}, "outputs": {"output_hap": {"id": "ee8e3ca83e5a4f34", "src": "hda", "uuid": "45ff78c2-c0b4-4633-9ee0-13ffeacb3c5d"}, "output_legend": {"id": "3ff5d0b134e63ad6", "src": "hda", "uuid": "ba076ec3-fb09-48e7-adb8-38d9945ada03"}, "output_samples": {"id": "8c52fb4098cc199f", "src": "hda", "uuid": "d9c6b2b6-182e-4e8b-b051-40534e36c16a"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Hap file: /galaxy/server/database/objects/4/5/f/dataset_45ff78c2-c0b4-4633-9ee0-13ffeacb3c5d.dat\nLegend file: /galaxy/server/database/objects/b/a/0/dataset_ba076ec3-fb09-48e7-adb8-38d9945ada03.dat\nSample file: /galaxy/server/database/objects/d/9/c/dataset_d9c6b2b6-182e-4e8b-b051-40534e36c16a.dat\nWarning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n32 records written, 1 skipped: 0/1/0 no-ALT/non-biallelic/filtered\n", "job_stdout": "", "job_stderr": "", "stderr": "Hap file: /galaxy/server/database/objects/4/5/f/dataset_45ff78c2-c0b4-4633-9ee0-13ffeacb3c5d.dat\nLegend file: /galaxy/server/database/objects/b/a/0/dataset_ba076ec3-fb09-48e7-adb8-38d9945ada03.dat\nSample file: /galaxy/server/database/objects/d/9/c/dataset_d9c6b2b6-182e-4e8b-b051-40534e36c16a.dat\nWarning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n32 records written, 1 skipped: 0/1/0 no-ALT/non-biallelic/filtered\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": "2024-09-23 13:24:06", "plugin": "core", "name": "end_epoch", "raw_value": "1727097846.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:24:05", "plugin": "core", "name": "start_epoch", "raw_value": "1727097845.0000000"}, {"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_convert_from_vcf/1.15.1+galaxy4-5", "has_data": true, "data": {"tool_id": "bcftools_convert_from_vcf", "tool_version": "1.15.1+galaxy4", "test_index": 5, "time_seconds": 34.025845766067505, "inputs": {"input_file": {"src": "hda", "id": "a06da25ef9238f7e"}, "keep_duplicates": true, "convert|convert_to": "hap_legend_sample"}, "job": {"model_class": "Job", "id": "9ee744f7a0e794d0", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:24:51.623490", "create_time": "2024-09-23T13:24:38.933581", "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_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4", "history_id": "947bb6702479ed20", "external_id": "gxy-7jvnb", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/3/1/3/dataset_313e07f5-5096-417a-9e15-8b1daec050a6.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools convert --haplegendsample \"/galaxy/server/database/objects/0/6/2/dataset_0620eefa-46ac-4cbd-a4e1-dfa8f0339a82.dat,/galaxy/server/database/objects/c/3/e/dataset_c3eca974-0829-49cf-a26f-5fb4a24057ed.dat,/galaxy/server/database/objects/7/6/1/dataset_76164eed-2403-4071-84ed-bfeb3fc1c71e.dat\" --keep-duplicates --keep-duplicates \"/galaxy/server/database/objects/3/1/3/dataset_313e07f5-5096-417a-9e15-8b1daec050a6.dat\" .", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "convert": "{\"__current_case__\": 2, \"convert_to\": \"hap_legend_sample\", \"haploid2diploid\": false, \"sex_info\": {\"__current_case__\": 0, \"sex_info_src\": \"none\"}, \"vcf_ids\": false}", "keep_duplicates": "true", "sec_restrict": "{\"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "a06da25ef9238f7e", "src": "hda", "uuid": "313e07f5-5096-417a-9e15-8b1daec050a6"}}, "outputs": {"output_hap": {"id": "4c23b56a0bbae1e0", "src": "hda", "uuid": "0620eefa-46ac-4cbd-a4e1-dfa8f0339a82"}, "output_legend": {"id": "fc775a1a6a94d00b", "src": "hda", "uuid": "c3eca974-0829-49cf-a26f-5fb4a24057ed"}, "output_samples": {"id": "5883611758cae18b", "src": "hda", "uuid": "76164eed-2403-4071-84ed-bfeb3fc1c71e"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Hap file: /galaxy/server/database/objects/0/6/2/dataset_0620eefa-46ac-4cbd-a4e1-dfa8f0339a82.dat\nLegend file: /galaxy/server/database/objects/c/3/e/dataset_c3eca974-0829-49cf-a26f-5fb4a24057ed.dat\nSample file: /galaxy/server/database/objects/7/6/1/dataset_76164eed-2403-4071-84ed-bfeb3fc1c71e.dat\nWarning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n32 records written, 1 skipped: 0/1/0 no-ALT/non-biallelic/filtered\n", "job_stdout": "", "job_stderr": "", "stderr": "Hap file: /galaxy/server/database/objects/0/6/2/dataset_0620eefa-46ac-4cbd-a4e1-dfa8f0339a82.dat\nLegend file: /galaxy/server/database/objects/c/3/e/dataset_c3eca974-0829-49cf-a26f-5fb4a24057ed.dat\nSample file: /galaxy/server/database/objects/7/6/1/dataset_76164eed-2403-4071-84ed-bfeb3fc1c71e.dat\nWarning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n32 records written, 1 skipped: 0/1/0 no-ALT/non-biallelic/filtered\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": "2024-09-23 13:24:41", "plugin": "core", "name": "end_epoch", "raw_value": "1727097881.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:24:40", "plugin": "core", "name": "start_epoch", "raw_value": "1727097880.0000000"}, {"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_convert_from_vcf/1.15.1+galaxy4-6", "has_data": true, "data": {"tool_id": "bcftools_convert_from_vcf", "tool_version": "1.15.1+galaxy4", "test_index": 6, "time_seconds": 33.79130935668945, "inputs": {"input_file": {"src": "hda", "id": "44c409b692a5accf"}, "sec_restrict|regions_overlap": "1", "convert|convert_to": "gen_sample"}, "job": {"model_class": "Job", "id": "5fb3644165b8d6c5", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:25:26.315941", "create_time": "2024-09-23T13:25:13.474212", "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_convert_from_vcf/bcftools_convert_from_vcf/1.15.1+galaxy4", "history_id": "947bb6702479ed20", "external_id": "gxy-c9pts", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/b/5/dataset_fb5bac14-e224-4b2c-8f73-84cba782c0dd.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools convert --tag GT --gensample \"/galaxy/server/database/objects/8/8/1/dataset_881ec19c-cf90-413a-b3c6-126f1c407e82.dat,/galaxy/server/database/objects/d/d/a/dataset_dda5e273-8ed4-41cf-85fd-85126840a19b.dat\" --regions-overlap 1 \"/galaxy/server/database/objects/f/b/5/dataset_fb5bac14-e224-4b2c-8f73-84cba782c0dd.dat\" .", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "convert": "{\"__current_case__\": 0, \"convert_3N6\": false, \"convert_to\": \"gen_sample\", \"sex_info\": {\"__current_case__\": 0, \"sex_info_src\": \"none\"}, \"tag\": \"GT\", \"vcf_ids\": false}", "keep_duplicates": "false", "sec_restrict": "{\"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": \"1\", \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "44c409b692a5accf", "src": "hda", "uuid": "fb5bac14-e224-4b2c-8f73-84cba782c0dd"}}, "outputs": {"output_gen": {"id": "6777be6dd9e98367", "src": "hda", "uuid": "881ec19c-cf90-413a-b3c6-126f1c407e82"}, "output_samples": {"id": "7117101ac9e6e9a8", "src": "hda", "uuid": "dda5e273-8ed4-41cf-85fd-85126840a19b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Gen file: /galaxy/server/database/objects/8/8/1/dataset_881ec19c-cf90-413a-b3c6-126f1c407e82.dat\nSample file: /galaxy/server/database/objects/d/d/a/dataset_dda5e273-8ed4-41cf-85fd-85126840a19b.dat\nWarning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n32 records written, 1 skipped: 0/1/0/0 no-ALT/non-biallelic/filtered/duplicated\n", "job_stdout": "", "job_stderr": "", "stderr": "Gen file: /galaxy/server/database/objects/8/8/1/dataset_881ec19c-cf90-413a-b3c6-126f1c407e82.dat\nSample file: /galaxy/server/database/objects/d/d/a/dataset_dda5e273-8ed4-41cf-85fd-85126840a19b.dat\nWarning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n32 records written, 1 skipped: 0/1/0/0 no-ALT/non-biallelic/filtered/duplicated\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": "2024-09-23 13:25:16", "plugin": "core", "name": "end_epoch", "raw_value": "1727097916.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:25:15", "plugin": "core", "name": "start_epoch", "raw_value": "1727097915.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_plugin_dosage/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_plugin_dosage", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 33.24185109138489, "inputs": {"input_file": {"src": "hda", "id": "526394ae6023d7d0"}}, "job": {"model_class": "Job", "id": "d4b3fc3e8e3a2639", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:26:01.551739", "create_time": "2024-09-23T13:25:47.802200", "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_dosage/bcftools_plugin_dosage/1.15.1+galaxy4", "history_id": "947bb6702479ed20", "external_id": "gxy-66fgd", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/1/3/3/dataset_1334c376-6ae8-4bef-957a-f4678704aed7.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin dosage input.vcf.gz > '/galaxy/server/database/objects/4/4/a/dataset_44a37551-0b80-48f2-8062-863b47045e53.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_plugin": "{\"tags\": \"\"}", "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": "526394ae6023d7d0", "src": "hda", "uuid": "1334c376-6ae8-4bef-957a-f4678704aed7"}}, "outputs": {"output_file": {"id": "913ca56a11666b9b", "src": "hda", "uuid": "44a37551-0b80-48f2-8062-863b47045e53"}}, "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": "2024-09-23 13:25:50", "plugin": "core", "name": "end_epoch", "raw_value": "1727097950.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:25:50", "plugin": "core", "name": "start_epoch", "raw_value": "1727097950.0000000"}, {"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": "bwameth/0.2.7+galaxy0-0", "has_data": true, "data": {"tool_id": "bwameth", "tool_version": "0.2.7+galaxy0", "test_index": 0, "time_seconds": 2061.8117706775665, "inputs": {"referenceSource|reference": {"src": "hda", "id": "f8c781446a345c70"}, "referenceSource|source": "history", "single_or_paired|input_mate1": {"src": "hda", "id": "2dd39c81427ee5bd"}, "single_or_paired|input_mate2": {"src": "hda", "id": "05ccd5f464c64737"}, "single_or_paired|single_or_paired_opts": "paired"}, "job": {"model_class": "Job", "id": "a06da25ef9238f7e", "state": "paused", "exit_code": null, "update_time": "2024-09-23T13:30:44.909844", "create_time": "2024-09-23T13:30:39.976109", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0", "history_id": "947bb6702479ed20", "external_id": null, "command_line": null, "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "readGroup": "\"\"", "single_or_paired": "{\"__current_case__\": 1, \"input_mate1\": {\"values\": [{\"id\": 173, \"src\": \"hda\"}]}, \"input_mate2\": {\"values\": [{\"id\": 174, \"src\": \"hda\"}]}, \"single_or_paired_opts\": \"paired\"}", "referenceSource": "{\"__current_case__\": 0, \"reference\": {\"values\": [{\"id\": 175, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"referenceSource|reference": {"id": "d7578f35ab2a3690", "src": "hda", "uuid": "1fb8e9d9-ea79-42f3-b81a-8a936e04c841"}, "single_or_paired|input_mate1": {"id": "2dd39c81427ee5bd", "src": "hda", "uuid": "2a831fd0-5c5e-4955-959e-94ef14b88e8e"}, "single_or_paired|input_mate2": {"id": "05ccd5f464c64737", "src": "hda", "uuid": "330fc1a1-b134-4abd-9113-a87587200e01"}}, "outputs": {"output": {"id": "fb7603d2b2400d35", "src": "hda", "uuid": "5737af86-0013-432e-8f21-7b8744093a6b"}}, "output_collections": {}, "tool_stdout": null, "tool_stderr": null, "job_stdout": null, "job_stderr": null, "stderr": "", "stdout": "", "job_messages": null, "dependencies": [], "user_email": "tests@fake.org", "job_metrics": []}, "output_problems": ["Timed out after 600.25 seconds waiting on tool test run.", "Timed out after 600.25 seconds waiting on tool test run."], "status": "failure"}}, {"id": "bwameth/0.2.7+galaxy0-1", "has_data": true, "data": {"tool_id": "bwameth", "tool_version": "0.2.7+galaxy0", "test_index": 1, "time_seconds": 85.72240161895752, "inputs": {"referenceSource|reference": {"src": "hda", "id": "9c2da9cdccc786a4"}, "referenceSource|source": "history", "single_or_paired|input_mate1": {"src": "hdca", "id": "b849e135bbda4f49"}, "single_or_paired|single_or_paired_opts": "paired_collection"}, "job": {"model_class": "Job", "id": "6777be6dd9e98367", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T14:06:02.074209", "create_time": "2024-09-23T14:05:02.140879", "galaxy_version": "23.1", "command_version": "bwa-meth.py 0.2.7", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0", "history_id": "947bb6702479ed20", "external_id": "gxy-bmckk", "command_line": "mkdir index_dir && ln -s '/galaxy/server/database/objects/a/4/6/dataset_a4675d0a-8f15-4696-a9f6-0c5c1c045ecc.dat' index_dir/genome.fa && bwameth.py index index_dir/genome.fa && ln -s '/galaxy/server/database/objects/c/9/3/dataset_c93f1ba8-3dbd-4f1e-a872-3342f29e844a.dat' input_f.fastq.gz && ln -s '/galaxy/server/database/objects/c/7/1/dataset_c7128ff4-a847-484b-81cd-ec10583fb493.dat' input_r.fastq.gz && bwameth.py -t \"${GALAXY_SLOTS:-4}\" --reference 'index_dir/genome.fa' input_f.fastq.gz input_r.fastq.gz | samtools sort -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view -O bam -@ ${GALAXY_SLOTS:-1} -o output.bam", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "readGroup": "\"\"", "single_or_paired": "{\"__current_case__\": 2, \"input_mate1\": {\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}, \"single_or_paired_opts\": \"paired_collection\"}", "referenceSource": "{\"__current_case__\": 0, \"reference\": {\"values\": [{\"id\": 180, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"referenceSource|reference": {"id": "69f1905304dd0ae7", "src": "hda", "uuid": "a4675d0a-8f15-4696-a9f6-0c5c1c045ecc"}, "single_or_paired|input_mate11": {"id": "85bb1ff0c5d7280e", "src": "hda", "uuid": "c93f1ba8-3dbd-4f1e-a872-3342f29e844a"}, "single_or_paired|input_mate12": {"id": "cbb3f60beffe998d", "src": "hda", "uuid": "c7128ff4-a847-484b-81cd-ec10583fb493"}}, "outputs": {"output": {"id": "af0082cf72685792", "src": "hda", "uuid": "6b00e2d0-0371-4e62-88c3-b92d56a93afe"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "converting c2t in index_dir/genome.fa to index_dir/genome.fa.bwameth.c2t\nindexing with bwa-mem: index_dir/genome.fa.bwameth.c2t\n[bwa_index] Pack FASTA... 0.02 sec\n[bwa_index] Construct BWT for the packed sequence...\n[BWTIncCreate] textLength=3600000, availableWord=4573648\n[bwt_gen] Finished constructing BWT in 5 iterations.\n[bwa_index] 0.93 seconds elapse.\n[bwa_index] Update BWT... 0.01 sec\n[bwa_index] Pack forward-only FASTA... 0.01 sec\n[bwa_index] Construct SA from BWT and Occ... 0.21 sec\n[main] Version: 0.7.17-r1188\n[main] CMD: bwa index -a bwtsw index_dir/genome.fa.bwameth.c2t\n[main] Real time: 1.319 sec; CPU: 1.189 sec\n--------------------\nFound BWA MEM index\nrunning: /usr/local/bin/python /usr/local/bin/bwameth.py c2t input_f.fastq.gz input_r.fastq.gz |bwa mem -T 40 -B 2 -L 10 -CM -U 100 -p -R '@RG\\tID:input_\\tSM:input_' -t 8 index_dir/genome.fa.bwameth.c2t /dev/stdin\n--------------------\n[M::bwa_idx_load_from_disk] read 0 ALT contigs\nconverting reads in input_f.fastq.gz,input_r.fastq.gz\n[M::process] read 200 sequences (20200 bp)...\n[M::process] 0 single-end sequences; 200 paired-end sequences\n[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97, 0, 0)\n[M::mem_pestat] skip orientation FF as there are not enough pairs\n[M::mem_pestat] analyzing insert size distribution for orientation FR...\n[M::mem_pestat] (25, 50, 75) percentile: (108, 141, 169)\n[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 291)\n[M::mem_pestat] mean and std.dev: (138.16, 39.31)\n[M::mem_pestat] low and high boundaries for proper pairs: (1, 352)\n[M::mem_pestat] skip orientation RF as there are not enough pairs\n[M::mem_pestat] skip orientation RR as there are not enough pairs\n[M::mem_process_seqs] Processed 200 reads in 0.030 CPU sec, 0.010 real sec\n[main] Version: 0.7.17-r1188\n[main] CMD: bwa mem -T 40 -B 2 -L 10 -CM -U 100 -p -R @RG\\tID:input_\\tSM:input_ -t 8 index_dir/genome.fa.bwameth.c2t /dev/stdin\n[main] Real time: 0.146 sec; CPU: 0.038 sec\n", "job_stdout": "", "job_stderr": "", "stderr": "converting c2t in index_dir/genome.fa to index_dir/genome.fa.bwameth.c2t\nindexing with bwa-mem: index_dir/genome.fa.bwameth.c2t\n[bwa_index] Pack FASTA... 0.02 sec\n[bwa_index] Construct BWT for the packed sequence...\n[BWTIncCreate] textLength=3600000, availableWord=4573648\n[bwt_gen] Finished constructing BWT in 5 iterations.\n[bwa_index] 0.93 seconds elapse.\n[bwa_index] Update BWT... 0.01 sec\n[bwa_index] Pack forward-only FASTA... 0.01 sec\n[bwa_index] Construct SA from BWT and Occ... 0.21 sec\n[main] Version: 0.7.17-r1188\n[main] CMD: bwa index -a bwtsw index_dir/genome.fa.bwameth.c2t\n[main] Real time: 1.319 sec; CPU: 1.189 sec\n--------------------\nFound BWA MEM index\nrunning: /usr/local/bin/python /usr/local/bin/bwameth.py c2t input_f.fastq.gz input_r.fastq.gz |bwa mem -T 40 -B 2 -L 10 -CM -U 100 -p -R '@RG\\tID:input_\\tSM:input_' -t 8 index_dir/genome.fa.bwameth.c2t /dev/stdin\n--------------------\n[M::bwa_idx_load_from_disk] read 0 ALT contigs\nconverting reads in input_f.fastq.gz,input_r.fastq.gz\n[M::process] read 200 sequences (20200 bp)...\n[M::process] 0 single-end sequences; 200 paired-end sequences\n[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97, 0, 0)\n[M::mem_pestat] skip orientation FF as there are not enough pairs\n[M::mem_pestat] analyzing insert size distribution for orientation FR...\n[M::mem_pestat] (25, 50, 75) percentile: (108, 141, 169)\n[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 291)\n[M::mem_pestat] mean and std.dev: (138.16, 39.31)\n[M::mem_pestat] low and high boundaries for proper pairs: (1, 352)\n[M::mem_pestat] skip orientation RF as there are not enough pairs\n[M::mem_pestat] skip orientation RR as there are not enough pairs\n[M::mem_process_seqs] Processed 200 reads in 0.030 CPU sec, 0.010 real sec\n[main] Version: 0.7.17-r1188\n[main] CMD: bwa mem -T 40 -B 2 -L 10 -CM -U 100 -p -R @RG\\tID:input_\\tSM:input_ -t 8 index_dir/genome.fa.bwameth.c2t /dev/stdin\n[main] Real time: 0.146 sec; CPU: 0.038 sec\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": "2024-09-23 14:05:50", "plugin": "core", "name": "end_epoch", "raw_value": "1727100350.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 14:05:48", "plugin": "core", "name": "start_epoch", "raw_value": "1727100348.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "deeptools_correct_gc_bias/3.5.4+galaxy0-0", "has_data": true, "data": {"tool_id": "deeptools_correct_gc_bias", "tool_version": "3.5.4+galaxy0", "test_index": 0, "time_seconds": 58.19691014289856, "inputs": {"GCbiasFrequenciesFile": {"src": "hda", "id": "e889621d1cf56dac"}, "bamInput": {"src": "hda", "id": "a550e85499a827e7"}, "source|input1": {"src": "hda", "id": "e408a4d2384943e7"}, "source|ref_source": "history", "effectiveGenomeSize|effectiveGenomeSize": "10050", "effectiveGenomeSize|effectiveGenomeSize_opt": "specific"}, "job": {"model_class": "Job", "id": "9cdc6b8f809b4df7", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:30:12.200398", "create_time": "2024-09-23T13:29:40.288153", "galaxy_version": "23.1", "command_version": "correctGCBias 3.5.4", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.5.4+galaxy0", "history_id": "947bb6702479ed20", "external_id": "gxy-p47ms", "command_line": "ln -s '/galaxy/server/database/objects/d/f/4/dataset_df406e63-2f83-411b-8a0d-5f38b86b9db7.dat' local_bamInput.bam && ln -s '/galaxy/server/database/objects/_metadata_files/0/c/1/metadata_0c13f28f-b092-4993-b626-48f354d61c24.dat' local_bamInput.bam.bai && correctGCBias --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bamfile local_bamInput.bam --GCbiasFrequenciesFile '/galaxy/server/database/objects/8/8/c/dataset_88c299fa-d100-4b75-95c8-09916aa0cef9.dat' --genome /galaxy/server/database/objects/6/d/a/dataset_6da872a5-e0a9-4c52-8130-6aab691d047f.dat --effectiveGenomeSize 10050 --correctedFile corrected.bam", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "region": "\"\"", "effectiveGenomeSize": "{\"__current_case__\": 0, \"effectiveGenomeSize\": \"10050\", \"effectiveGenomeSize_opt\": \"specific\"}", "source": "{\"__current_case__\": 1, \"input1\": {\"values\": [{\"id\": 170, \"src\": \"hda\"}]}, \"ref_source\": \"history\"}"}, "inputs": {"GCbiasFrequenciesFile": {"id": "e889621d1cf56dac", "src": "hda", "uuid": "88c299fa-d100-4b75-95c8-09916aa0cef9"}, "bamInput": {"id": "a550e85499a827e7", "src": "hda", "uuid": "df406e63-2f83-411b-8a0d-5f38b86b9db7"}, "source|input1": {"id": "e408a4d2384943e7", "src": "hda", "uuid": "6da872a5-e0a9-4c52-8130-6aab691d047f"}}, "outputs": {"outFileName": {"id": "d7ca9d1686fa5af5", "src": "hda", "uuid": "f2486d94-c61e-4858-aa17-e0b19140b9d4"}}, "output_collections": {}, "tool_stdout": "applying correction\ngenome partition size for multiprocessing: 319326\nusing region None\n{'chr2L': 'chr2L'} {'chr2L': 'chr2L'}\nusing 8 processors for 73 number of tasks\nconcatenating (sorted) intermediate BAMs\nindexing BAM\nSam for chr2L 5747868 6067194 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:5747868-6067194\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 6067194 6386520 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:6067194-6386520\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 6386520 6705846 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:6386520-6705846\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 10537758 10857084 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:10537758-10857084\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 10857084 11176410 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:10857084-11176410\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 11176410 11495736 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:11176410-11495736\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 16285626 16604952 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:16285626-16604952\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 16604952 16924278 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:16604952-16924278\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 16924278 17243604 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:16924278-17243604\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 1915956 2235282 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:1915956-2235282\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 2235282 2554608 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:2235282-2554608\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 2554608 2873934 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:2554608-2873934\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 11495736 11815062 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:11495736-11815062\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 11815062 12134388 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:11815062-12134388\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 12134388 12453714 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:12134388-12453714\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 18201582 18520908 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:18201582-18520908\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 18520908 18840234 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:18520908-18840234\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 18840234 19159560 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:18840234-19159560\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 4789890 5109216 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:4789890-5109216\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 5109216 5428542 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:5109216-5428542\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 5428542 5747868 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:5428542-5747868\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 9579780 9899106 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:9579780-9899106\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 9899106 10218432 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:9899106-10218432\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 10218432 10537758 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:10218432-10537758\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 17243604 17562930 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:17243604-17562930\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 17562930 17882256 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:17562930-17882256\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 17882256 18201582 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:17882256-18201582\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 22991472 23011544 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:22991472-23011544\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 6705846 7025172 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:6705846-7025172\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 7025172 7344498 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:7025172-7344498\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 7344498 7663824 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:7344498-7663824\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 12453714 12773040 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:12453714-12773040\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 12773040 13092366 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:12773040-13092366\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 13092366 13411692 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:13092366-13411692\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 20117538 20436864 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:20117538-20436864\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 20436864 20756190 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:20436864-20756190\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 20756190 21075516 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:20756190-21075516\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 2873934 3193260 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:2873934-3193260\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 3193260 3512586 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:3193260-3512586\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 3512586 3831912 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:3512586-3831912\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 13411692 13731018 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:13411692-13731018\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 13731018 14050344 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:13731018-14050344\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 14050344 14369670 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:14050344-14369670\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 19159560 19478886 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:19159560-19478886\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 19478886 19798212 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:19478886-19798212\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 19798212 20117538 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:19798212-20117538\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 957978 1277304 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:957978-1277304\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 1277304 1596630 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:1277304-1596630\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 1596630 1915956 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:1596630-1915956\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 7663824 7983150 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:7663824-7983150\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 7983150 8302476 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:7983150-8302476\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 8302476 8621802 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:8302476-8621802\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 14369670 14688996 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:14369670-14688996\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 14688996 15008322 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:14688996-15008322\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 15008322 15327648 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:15008322-15327648\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 21075516 21394842 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:21075516-21394842\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 21394842 21714168 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:21394842-21714168\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 21714168 22033494 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:21714168-22033494\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 3831912 4151238 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:3831912-4151238\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 4151238 4470564 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:4151238-4470564\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 4470564 4789890 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:4470564-4789890\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 8621802 8941128 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:8621802-8941128\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 8941128 9260454 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:8941128-9260454\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 9260454 9579780 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:9260454-9579780\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 15327648 15646974 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:15327648-15646974\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 15646974 15966300 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:15646974-15966300\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 15966300 16285626 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:15966300-16285626\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 22033494 22352820 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:22033494-22352820\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 22352820 22672146 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:22352820-22672146\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 22672146 22991472 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:22672146-22991472\nduplicated reads removed 0 of 0 (0.00) \n", "tool_stderr": "[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_t3d70d5z.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_t3d70d5z.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_why1xzlq.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_13915v9_.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_54jtgqny.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__axce_0v.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_w5bb9w7a.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_v2nzjpdx.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_7rf_k4lg.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_v6lbq4vg.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__9cjwc3m.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_n_i1zbjs.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_9em0t16e.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_k8mmqnvs.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__mjdqsk8.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__apcgv3o.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_u8zokofb.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_1xk_gdq7.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_dc4qmbcr.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_rznv_ah5.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_ib0z6mni.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__swm8t2e.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_75al10lu.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_6pt2l4lu.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_d0_xqwlh.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_scbivdr4.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_wipfmq1d.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_o3_m4jek.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_125x9eze.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_o5qy4kzt.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_vxymhuc6.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_0jg73xxf.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_8dy639sb.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_snrm7jb1.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__jrnu5v7.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_452mpjzj.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_qrv08gpw.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_9iapb8yd.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_6_rj_mme.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_8bzaiajs.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_w9v1ll3h.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_frsfa4sf.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__szy68et.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_qf9fegvb.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_fsr1eel4.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_6o1aj4jo.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_ntia6q1l.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__jvkjpcw.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_vgv5npfw.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_rb_fv4cn.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_j2kkr6f1.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_ohdmpz6d.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_g2u40lz1.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_yggao1mu.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_xmnvvp6x.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_ogg46nzl.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_3zwm1dcv.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_25weqtp3.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_n5xt58qa.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_2vd6blav.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_a3ilq52z.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_zeaixnr_.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_m4nvrs4r.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_pctcnddw.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_k6omc4wf.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_h4_p96ey.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_kzr08jui.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_bg0zqro6.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_z90tm6cp.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_y37kum6s.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_ejn9dwsq.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_z6i2yhrq.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_q0rwd11q.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_xx05mxfs.bam'\n", "job_stdout": "", "job_stderr": "", "stderr": "[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_t3d70d5z.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_t3d70d5z.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_why1xzlq.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_13915v9_.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_54jtgqny.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__axce_0v.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_w5bb9w7a.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_v2nzjpdx.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_7rf_k4lg.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_v6lbq4vg.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__9cjwc3m.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_n_i1zbjs.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_9em0t16e.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_k8mmqnvs.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__mjdqsk8.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__apcgv3o.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_u8zokofb.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_1xk_gdq7.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_dc4qmbcr.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_rznv_ah5.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_ib0z6mni.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__swm8t2e.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_75al10lu.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_6pt2l4lu.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_d0_xqwlh.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_scbivdr4.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_wipfmq1d.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_o3_m4jek.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_125x9eze.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_o5qy4kzt.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_vxymhuc6.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_0jg73xxf.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_8dy639sb.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_snrm7jb1.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__jrnu5v7.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_452mpjzj.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_qrv08gpw.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_9iapb8yd.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_6_rj_mme.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_8bzaiajs.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_w9v1ll3h.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_frsfa4sf.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__szy68et.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_qf9fegvb.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_fsr1eel4.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_6o1aj4jo.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_ntia6q1l.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools__jvkjpcw.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_vgv5npfw.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_rb_fv4cn.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_j2kkr6f1.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_ohdmpz6d.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_g2u40lz1.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_yggao1mu.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_xmnvvp6x.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_ogg46nzl.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_3zwm1dcv.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_25weqtp3.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_n5xt58qa.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_2vd6blav.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_a3ilq52z.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_zeaixnr_.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_m4nvrs4r.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_pctcnddw.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_k6omc4wf.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_h4_p96ey.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_kzr08jui.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_bg0zqro6.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_z90tm6cp.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_y37kum6s.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_ejn9dwsq.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_z6i2yhrq.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_q0rwd11q.bam'\n[E::idx_find_and_load] Could not retrieve index file for '/galaxy/server/database/jobs_directory/000/143/tmp/_deeptools_xx05mxfs.bam'\n", "stdout": "applying correction\ngenome partition size for multiprocessing: 319326\nusing region None\n{'chr2L': 'chr2L'} {'chr2L': 'chr2L'}\nusing 8 processors for 73 number of tasks\nconcatenating (sorted) intermediate BAMs\nindexing BAM\nSam for chr2L 5747868 6067194 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:5747868-6067194\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 6067194 6386520 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:6067194-6386520\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 6386520 6705846 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:6386520-6705846\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 10537758 10857084 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:10537758-10857084\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 10857084 11176410 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:10857084-11176410\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 11176410 11495736 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:11176410-11495736\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 16285626 16604952 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:16285626-16604952\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 16604952 16924278 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:16604952-16924278\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 16924278 17243604 \nForkPoolWorker-7, processing 0 (0.0 per sec) reads @ chr2L:16924278-17243604\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 1915956 2235282 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:1915956-2235282\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 2235282 2554608 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:2235282-2554608\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 2554608 2873934 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:2554608-2873934\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 11495736 11815062 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:11495736-11815062\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 11815062 12134388 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:11815062-12134388\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 12134388 12453714 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:12134388-12453714\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 18201582 18520908 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:18201582-18520908\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 18520908 18840234 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:18520908-18840234\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 18840234 19159560 \nForkPoolWorker-3, processing 0 (0.0 per sec) reads @ chr2L:18840234-19159560\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 4789890 5109216 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:4789890-5109216\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 5109216 5428542 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:5109216-5428542\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 5428542 5747868 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:5428542-5747868\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 9579780 9899106 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:9579780-9899106\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 9899106 10218432 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:9899106-10218432\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 10218432 10537758 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:10218432-10537758\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 17243604 17562930 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:17243604-17562930\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 17562930 17882256 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:17562930-17882256\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 17882256 18201582 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:17882256-18201582\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 22991472 23011544 \nForkPoolWorker-6, processing 0 (0.0 per sec) reads @ chr2L:22991472-23011544\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 6705846 7025172 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:6705846-7025172\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 7025172 7344498 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:7025172-7344498\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 7344498 7663824 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:7344498-7663824\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 12453714 12773040 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:12453714-12773040\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 12773040 13092366 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:12773040-13092366\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 13092366 13411692 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:13092366-13411692\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 20117538 20436864 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:20117538-20436864\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 20436864 20756190 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:20436864-20756190\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 20756190 21075516 \nForkPoolWorker-8, processing 0 (0.0 per sec) reads @ chr2L:20756190-21075516\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 2873934 3193260 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:2873934-3193260\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 3193260 3512586 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:3193260-3512586\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 3512586 3831912 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:3512586-3831912\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 13411692 13731018 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:13411692-13731018\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 13731018 14050344 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:13731018-14050344\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 14050344 14369670 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:14050344-14369670\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 19159560 19478886 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:19159560-19478886\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 19478886 19798212 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:19478886-19798212\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 19798212 20117538 \nForkPoolWorker-4, processing 0 (0.0 per sec) reads @ chr2L:19798212-20117538\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 957978 1277304 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:957978-1277304\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 1277304 1596630 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:1277304-1596630\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 1596630 1915956 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:1596630-1915956\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 7663824 7983150 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:7663824-7983150\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 7983150 8302476 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:7983150-8302476\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 8302476 8621802 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:8302476-8621802\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 14369670 14688996 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:14369670-14688996\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 14688996 15008322 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:14688996-15008322\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 15008322 15327648 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:15008322-15327648\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 21075516 21394842 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:21075516-21394842\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 21394842 21714168 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:21394842-21714168\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 21714168 22033494 \nForkPoolWorker-2, processing 0 (0.0 per sec) reads @ chr2L:21714168-22033494\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 3831912 4151238 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:3831912-4151238\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 4151238 4470564 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:4151238-4470564\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 4470564 4789890 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:4470564-4789890\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 8621802 8941128 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:8621802-8941128\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 8941128 9260454 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:8941128-9260454\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 9260454 9579780 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:9260454-9579780\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 15327648 15646974 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:15327648-15646974\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 15646974 15966300 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:15646974-15966300\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 15966300 16285626 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:15966300-16285626\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 22033494 22352820 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:22033494-22352820\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 22352820 22672146 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:22352820-22672146\nduplicated reads removed 0 of 0 (0.00) \nSam for chr2L 22672146 22991472 \nForkPoolWorker-5, processing 0 (0.0 per sec) reads @ chr2L:22672146-22991472\nduplicated reads removed 0 of 0 (0.00) \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": "2024-09-23 13:29:58", "plugin": "core", "name": "end_epoch", "raw_value": "1727098198.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:29:55", "plugin": "core", "name": "start_epoch", "raw_value": "1727098195.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "edger/3.36.0+galaxy5-0", "has_data": true, "data": {"tool_id": "edger", "tool_version": "3.36.0+galaxy5", "test_index": 0, "time_seconds": 56.789231061935425, "inputs": {"input|counts": {"src": "hda", "id": "2bdde901cf865f69"}, "input|fact|rep_factor_0|factorName": "Genotype", 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0, "update_time": "2024-09-23T13:05:57.154852", "create_time": "2024-09-23T13:05:44.194667", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-7vt26", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/9/d/0/dataset_9d001467-10f0-41eb-ad7a-1ee312e64690.dat' sanger '/galaxy/server/database/objects/0/f/d/dataset_0fdab37f-dce3-4356-ac81-7d5d83cfb875.dat' cssanger None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"cssanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"sanger\""}, "inputs": {"input_file": {"id": "dfa41e1c924687cb", "src": "hda", "uuid": "9d001467-10f0-41eb-ad7a-1ee312e64690"}}, "outputs": {"output_file": {"id": "48009a930b8487fd", "src": "hda", "uuid": "0fdab37f-dce3-4356-ac81-7d5d83cfb875"}}, "output_collections": {}, "tool_stdout": "Groomed 2 sanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 sanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "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": "2024-09-23 13:05:46", "plugin": "core", "name": "end_epoch", "raw_value": "1727096746.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:05:45", "plugin": "core", "name": "start_epoch", "raw_value": "1727096745.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-16", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 16, "time_seconds": 32.29331707954407, "inputs": {"input_file": {"src": "hda", "id": "6d0f65f4e5c34f24"}, "input_type": "solexa", "options_type|output_type": "solexa", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "d5a62abe1cd005d4", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:06:29.679450", "create_time": "2024-09-23T13:06:16.670641", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-wjxcw", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/5/f/6/dataset_5f67d3fa-4855-48a2-9941-10cdfafb9a32.dat' solexa '/galaxy/server/database/objects/4/a/1/dataset_4a1d4595-2ac9-4af3-b335-ce20d0cd0853.dat' solexa None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"solexa\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"solexa\""}, "inputs": {"input_file": {"id": "6d0f65f4e5c34f24", "src": "hda", "uuid": "5f67d3fa-4855-48a2-9941-10cdfafb9a32"}}, "outputs": {"output_file": {"id": "57067365a9ea695e", "src": "hda", "uuid": "4a1d4595-2ac9-4af3-b335-ce20d0cd0853"}}, "output_collections": {}, "tool_stdout": "Groomed 2 solexa reads into solexa reads.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 solexa reads into solexa reads.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "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": "2024-09-23 13:06:18", "plugin": "core", "name": "end_epoch", "raw_value": "1727096778.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:06:18", "plugin": "core", "name": "start_epoch", "raw_value": "1727096778.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-17", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 17, "time_seconds": 31.818020582199097, "inputs": {"input_file": {"src": "hda", "id": "9f26fccc1bbfb9c4"}, "input_type": "solexa", "options_type|output_type": "illumina", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "374937641cb6242d", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:07:01.855388", "create_time": "2024-09-23T13:06:50.351142", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-t5sq7", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/6/9/5/dataset_6952b739-a1e7-415f-be59-46e43d1ef7dd.dat' solexa '/galaxy/server/database/objects/5/4/5/dataset_545e7c7f-442a-40d8-87f4-00580f16921a.dat' illumina None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"illumina\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"solexa\""}, "inputs": {"input_file": {"id": "9f26fccc1bbfb9c4", "src": "hda", "uuid": "6952b739-a1e7-415f-be59-46e43d1ef7dd"}}, "outputs": {"output_file": {"id": "f51da42d371d039e", "src": "hda", "uuid": "545e7c7f-442a-40d8-87f4-00580f16921a"}}, "output_collections": {}, "tool_stdout": "Groomed 2 solexa reads into illumina reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 solexa reads into illumina reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "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": "2024-09-23 13:06:51", "plugin": "core", "name": "end_epoch", "raw_value": "1727096811.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:06:51", "plugin": "core", "name": "start_epoch", "raw_value": "1727096811.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-18", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 18, "time_seconds": 31.39230728149414, "inputs": {"input_file": {"src": "hda", "id": "1e862f876c47a0da"}, "input_type": "solexa", "options_type|output_type": "sanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "8dfb5501d2079009", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:07:33.164145", "create_time": "2024-09-23T13:07:21.465975", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-25mc9", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/8/7/4/dataset_874ba87a-2b03-4335-8e80-57bef178cf9b.dat' solexa '/galaxy/server/database/objects/8/c/b/dataset_8cb313b2-d0a5-461c-9092-fd07a34d961e.dat' sanger None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"solexa\""}, "inputs": {"input_file": {"id": "1e862f876c47a0da", "src": "hda", "uuid": "874ba87a-2b03-4335-8e80-57bef178cf9b"}}, "outputs": {"output_file": {"id": "bd18c3786bd9c47a", "src": "hda", "uuid": "8cb313b2-d0a5-461c-9092-fd07a34d961e"}}, "output_collections": {}, "tool_stdout": "Groomed 2 solexa reads into sanger reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 solexa reads into sanger reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "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": "2024-09-23 13:07:22", "plugin": "core", "name": "end_epoch", "raw_value": "1727096842.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:07:22", "plugin": "core", "name": "start_epoch", "raw_value": "1727096842.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-19", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 19, "time_seconds": 33.60253691673279, "inputs": {"input_file": {"src": "hda", "id": "9642d6f68834efd5"}, "input_type": "solexa", "options_type|output_type": "cssanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "9e9bef3212786702", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:08:07.033874", "create_time": "2024-09-23T13:07:53.880381", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-47kt6", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/c/d/e/dataset_cded1017-75ce-4cdb-af54-cd1a572247ab.dat' solexa '/galaxy/server/database/objects/9/3/5/dataset_9354412d-9673-41ff-82f9-89e46a5174af.dat' cssanger None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"cssanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"solexa\""}, "inputs": {"input_file": {"id": "9642d6f68834efd5", "src": "hda", "uuid": "cded1017-75ce-4cdb-af54-cd1a572247ab"}}, "outputs": {"output_file": {"id": "c37d3bcc697e9df0", "src": "hda", "uuid": "9354412d-9673-41ff-82f9-89e46a5174af"}}, "output_collections": {}, "tool_stdout": "Groomed 2 solexa reads into cssanger reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 solexa reads into cssanger reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "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": "2024-09-23 13:07:56", "plugin": "core", "name": "end_epoch", "raw_value": "1727096876.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:07:55", "plugin": "core", "name": "start_epoch", "raw_value": "1727096875.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-2", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 2, "time_seconds": 30.722145557403564, "inputs": {"input_file": {"src": "hda", "id": "b39635dd5af16c5f"}, "input_type": "sanger", "options_type|fix_id": false, "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "7956cb04120de21b", "state": "error", "exit_code": 1, "update_time": "2024-09-23T12:59:22.336268", "create_time": "2024-09-23T12:59:09.755571", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-4p88j", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/4/3/5/dataset_43579847-a887-42e8-bcfb-82cb86308b1c.dat' sanger '/galaxy/server/database/objects/4/f/8/dataset_4f883c4c-4e0e-439c-8b76-fe9918f340a6.dat' sanger ascii summarize_input --no-fix-id", "traceback": null, "params": {"input_type": "\"sanger\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": false, \"force_quality_encoding\": \"ascii\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "b39635dd5af16c5f", "src": "hda", "uuid": "43579847-a887-42e8-bcfb-82cb86308b1c"}}, "outputs": {"output_file": {"id": "254170a0185eab4b", "src": "hda", "uuid": "4f883c4c-4e0e-439c-8b76-fe9918f340a6"}}, "output_collections": {}, "tool_stdout": "There was an error reading your input file. Your input file is likely malformed.\nIt is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below.\nHowever, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism.\n\nThe reported error is: 'Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).'.\nThe error occurred at the start of your file and no valid FASTQ reads were found.\nThe error in your file occurs between lines '1' and '3', which corresponds to byte-offsets '0' and '33', and contains the text (33 of 33 bytes shown):\n\n@FAKE-1\nACGTACGTAC\n+invalid line\n\n", "tool_stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/gx-fastq-groomer\", line 10, in \n sys.exit(main())\n ^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 99, in main\n Groomer().run()\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 48, in run\n for read_count, fastq_read in enumerate(reader):\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 683, in __iter__\n yield next(self)\n ^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 742, in __next__\n raise e\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 724, in __next__\n block = super(fastqVerboseErrorReader, self).__next__()\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 621, in __next__\n self._read_fastq_sequence(rval, id_line)\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 666, in _read_fastq_sequence\n raise fastqFormatError(\ngalaxy_utils.sequence.fastq.fastqFormatError: Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).\n", "job_stdout": "", "job_stderr": "", "stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/gx-fastq-groomer\", line 10, in \n sys.exit(main())\n ^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 99, in main\n Groomer().run()\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_groomer.py\", line 48, in run\n for read_count, fastq_read in enumerate(reader):\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 683, in __iter__\n yield next(self)\n ^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 742, in __next__\n raise e\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 724, in __next__\n block = super(fastqVerboseErrorReader, self).__next__()\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 621, in __next__\n self._read_fastq_sequence(rval, id_line)\n File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/fastq.py\", line 666, in _read_fastq_sequence\n raise fastqFormatError(\ngalaxy_utils.sequence.fastq.fastqFormatError: Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).\n", "stdout": "There was an error reading your input file. Your input file is likely malformed.\nIt is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below.\nHowever, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism.\n\nThe reported error is: 'Invalid FASTQ file: quality score identifier (+invalid line) does not match sequence identifier (@FAKE-1).'.\nThe error occurred at the start of your file and no valid FASTQ reads were found.\nThe error in your file occurs between lines '1' and '3', which corresponds to byte-offsets '0' and '33', and contains the text (33 of 33 bytes shown):\n\n@FAKE-1\nACGTACGTAC\n+invalid line\n\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 12:59:11", "plugin": "core", "name": "start_epoch", "raw_value": "1727096351.0000000"}, {"title": "Job End Time", "value": "2024-09-23 12:59:11", "plugin": "core", "name": "end_epoch", "raw_value": "1727096351.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-20", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 20, "time_seconds": 33.17860674858093, "inputs": {"input_file": {"src": "hda", "id": "076271d24313dd49"}, "input_type": "cssanger", "options_type|output_type": "cssanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "74e9734e5ab1e351", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:08:40.267328", "create_time": "2024-09-23T13:08:26.796809", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-kx2ct", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/6/5/0/dataset_6507c126-e9b1-499f-831c-a8f4fe588d6b.dat' cssanger '/galaxy/server/database/objects/0/7/6/dataset_07611986-a6d3-4f4a-a075-7831123f6396.dat' cssanger None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"cssanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "076271d24313dd49", "src": "hda", "uuid": "6507c126-e9b1-499f-831c-a8f4fe588d6b"}}, "outputs": {"output_file": {"id": "c8562924fdbcf149", "src": "hda", "uuid": "07611986-a6d3-4f4a-a075-7831123f6396"}}, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "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": "2024-09-23 13:08:29", "plugin": "core", "name": "end_epoch", "raw_value": "1727096909.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:08:28", "plugin": "core", "name": "start_epoch", "raw_value": "1727096908.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-21", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 21, "time_seconds": 31.789817571640015, "inputs": {"input_file": {"src": "hda", "id": "c12415ed4ebe13a5"}, "input_type": "cssanger", "options_type|output_type": "sanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "f78423128d8952ce", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:09:12.434273", "create_time": "2024-09-23T13:09:00.059066", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-gvvjx", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/e/7/b/dataset_e7b11499-6e36-4e36-bbcd-a665f56589fc.dat' cssanger '/galaxy/server/database/objects/b/b/4/dataset_bb4a8047-eb20-4812-b74c-a2c56c17bc77.dat' sanger None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "c12415ed4ebe13a5", "src": "hda", "uuid": "e7b11499-6e36-4e36-bbcd-a665f56589fc"}}, "outputs": {"output_file": {"id": "bf07d796a754091e", "src": "hda", "uuid": "bb4a8047-eb20-4812-b74c-a2c56c17bc77"}}, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 cssanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "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": "2024-09-23 13:09:02", "plugin": "core", "name": "end_epoch", "raw_value": "1727096942.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:09:01", "plugin": "core", "name": "start_epoch", "raw_value": "1727096941.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-22", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 22, "time_seconds": 31.409193515777588, "inputs": {"input_file": {"src": "hda", "id": "e5c6fd44d073f013"}, "input_type": "cssanger", "options_type|output_type": "illumina", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "5fc5874de7554e71", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:09:43.860047", "create_time": "2024-09-23T13:09:31.231968", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-rxgz2", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/0/d/9/dataset_0d940641-a0bd-45af-bc8a-7eb38fc4098d.dat' cssanger '/galaxy/server/database/objects/7/9/0/dataset_7909b5ab-2650-40c2-9724-aea322f678e8.dat' illumina None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"illumina\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "e5c6fd44d073f013", "src": "hda", "uuid": "0d940641-a0bd-45af-bc8a-7eb38fc4098d"}}, "outputs": {"output_file": {"id": "0c6443eeb7a0fc27", "src": "hda", "uuid": "7909b5ab-2650-40c2-9724-aea322f678e8"}}, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into illumina reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 cssanger reads into illumina reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "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": "2024-09-23 13:09:33", "plugin": "core", "name": "end_epoch", "raw_value": "1727096973.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:09:33", "plugin": "core", "name": "start_epoch", "raw_value": "1727096973.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-23", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 23, "time_seconds": 32.59729361534119, "inputs": {"input_file": {"src": "hda", "id": "a650938ff37ae699"}, "input_type": "cssanger", "options_type|output_type": "solexa", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "79476c07c539c4c6", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:10:16.521754", "create_time": "2024-09-23T13:10:02.718222", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-f9fb7", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/e/5/9/dataset_e59c4b57-f072-41b5-b8c5-e38689933472.dat' cssanger '/galaxy/server/database/objects/b/0/0/dataset_b00b823e-2ef8-429d-b335-4fa8ed4569f4.dat' solexa None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"solexa\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "a650938ff37ae699", "src": "hda", "uuid": "e59c4b57-f072-41b5-b8c5-e38689933472"}}, "outputs": {"output_file": {"id": "78c81aba8ba91511", "src": "hda", "uuid": "b00b823e-2ef8-429d-b335-4fa8ed4569f4"}}, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into solexa reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 cssanger reads into solexa reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:10:04", "plugin": "core", "name": "start_epoch", "raw_value": "1727097004.0000000"}, {"title": "Job End Time", "value": "2024-09-23 13:10:05", "plugin": "core", "name": "end_epoch", "raw_value": "1727097005.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-24", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 24, "time_seconds": 32.200125217437744, "inputs": {"input_file": {"src": "hda", "id": "32a712ea8ae079d2"}, "input_type": "cssanger", "options_type|output_type": "cssanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "dfa41e1c924687cb", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:10:48.796934", "create_time": "2024-09-23T13:10:36.297207", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-9phxm", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/0/e/b/dataset_0eb9583f-6128-4139-b4c8-787420280d87.dat' cssanger '/galaxy/server/database/objects/1/8/2/dataset_18289f63-e5a2-4fb7-834c-51f9c275d68e.dat' cssanger None summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"cssanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "32a712ea8ae079d2", "src": "hda", "uuid": "0eb9583f-6128-4139-b4c8-787420280d87"}}, "outputs": {"output_file": {"id": "2fc6b8b216c7a7d4", "src": "hda", "uuid": "18289f63-e5a2-4fb7-834c-51f9c275d68e"}}, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - 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'F'(70)\nInput decimal range: 1 - 37\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 3 sanger reads into solexa reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '\"'(34) - 'F'(70)\nInput decimal range: 1 - 37\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:12:15", "plugin": "core", "name": "start_epoch", "raw_value": "1727097135.0000000"}, {"title": "Job End Time", "value": "2024-09-23 13:12:15", "plugin": "core", "name": "end_epoch", "raw_value": "1727097135.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-28", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 28, "time_seconds": 30.510241746902466, "inputs": {"input_file": {"src": "hda", "id": "df52d984be8780a7"}, "input_type": "sanger", "options_type|output_type": "sanger", "options_type|force_quality_encoding": "ascii", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "9642d6f68834efd5", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:12:57.575899", "create_time": "2024-09-23T13:12:45.504378", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-xqpkt", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/5/4/1/dataset_5418f339-093d-4055-b9ee-9b57fd0d18ba.dat' sanger '/galaxy/server/database/objects/c/2/e/dataset_c2e3d683-52d8-48be-9614-d33cf2dd2674.dat' sanger ascii summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"ascii\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"sanger\""}, "inputs": {"input_file": {"id": "df52d984be8780a7", "src": "hda", "uuid": "5418f339-093d-4055-b9ee-9b57fd0d18ba"}}, "outputs": {"output_file": {"id": "8464610a5411b770", "src": "hda", "uuid": "c2e3d683-52d8-48be-9614-d33cf2dd2674"}}, "output_collections": {}, "tool_stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:12:47", "plugin": "core", "name": "start_epoch", "raw_value": "1727097167.0000000"}, {"title": "Job End Time", "value": "2024-09-23 13:12:47", "plugin": "core", "name": "end_epoch", "raw_value": "1727097167.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-29", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 29, "time_seconds": 34.015475273132324, "inputs": {"input_file": {"src": "hda", "id": "d09b3ca03d880c63"}, "input_type": "sanger", "options_type|output_type": "sanger", "options_type|force_quality_encoding": "decimal", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "076271d24313dd49", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:13:31.765673", "create_time": "2024-09-23T13:13:18.359193", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-jjhh8", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/5/9/9/dataset_5990101a-7d2c-45ae-9fce-6f264444b4f9.dat' sanger '/galaxy/server/database/objects/3/c/2/dataset_3c24f4db-b47f-4bd0-8058-d46ac2406f7f.dat' sanger decimal summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"decimal\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"sanger\""}, "inputs": {"input_file": {"id": "d09b3ca03d880c63", "src": "hda", "uuid": "5990101a-7d2c-45ae-9fce-6f264444b4f9"}}, "outputs": {"output_file": {"id": "4446544aa0432b31", "src": "hda", "uuid": "3c24f4db-b47f-4bd0-8058-d46ac2406f7f"}}, "output_collections": {}, "tool_stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:13:20", "plugin": "core", "name": "start_epoch", "raw_value": "1727097200.0000000"}, {"title": "Job End Time", "value": "2024-09-23 13:13:20", "plugin": "core", "name": "end_epoch", "raw_value": "1727097200.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-3", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 3, "time_seconds": 33.0660605430603, "inputs": {"input_file": {"src": "hda", "id": "e91d5ceb9ba0cf60"}, "input_type": "sanger", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "df3c8fdfb989b284", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T12:59:54.865273", "create_time": "2024-09-23T12:59:41.935936", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-bd5q4", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/1/3/4/dataset_13428916-3ebf-44a6-b2b3-81f87551de20.dat' sanger '/galaxy/server/database/objects/a/8/3/dataset_a837d25a-b8f6-4164-8d3b-e75fe902a406.dat' sanger ascii summarize_input", "traceback": null, "params": {"input_type": "\"sanger\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "e91d5ceb9ba0cf60", "src": "hda", "uuid": "13428916-3ebf-44a6-b2b3-81f87551de20"}}, "outputs": {"output_file": {"id": "543711e0c33f7286", "src": "hda", "uuid": "a837d25a-b8f6-4164-8d3b-e75fe902a406"}}, "output_collections": {}, "tool_stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 12:59:44", "plugin": "core", "name": "start_epoch", "raw_value": "1727096384.0000000"}, {"title": "Job End Time", "value": "2024-09-23 12:59:44", "plugin": "core", "name": "end_epoch", "raw_value": "1727096384.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-30", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 30, "time_seconds": 33.19928193092346, "inputs": {"input_file": {"src": "hda", "id": "fedfaa8e7444a626"}, "input_type": "sanger", "options_type|output_type": "sanger", "options_type|force_quality_encoding": "ascii", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "c12415ed4ebe13a5", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:14:05.471794", "create_time": "2024-09-23T13:13:51.716224", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-99hrn", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/f/5/0/dataset_f50138dc-ddf1-45e7-aac4-57cafeedf73f.dat' sanger '/galaxy/server/database/objects/4/1/e/dataset_41ec9163-1c4e-4b3b-bd72-af3a1d63e275.dat' sanger ascii summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"ascii\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"sanger\""}, "inputs": {"input_file": {"id": "fedfaa8e7444a626", "src": "hda", "uuid": "f50138dc-ddf1-45e7-aac4-57cafeedf73f"}}, "outputs": {"output_file": {"id": "6b55f22a70f1a893", "src": "hda", "uuid": "41ec9163-1c4e-4b3b-bd72-af3a1d63e275"}}, "output_collections": {}, "tool_stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:13:53", "plugin": "core", "name": "start_epoch", "raw_value": "1727097233.0000000"}, {"title": "Job End Time", "value": "2024-09-23 13:13:53", "plugin": "core", "name": "end_epoch", "raw_value": "1727097233.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-31", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 31, "time_seconds": 30.63846468925476, "inputs": {"input_file": {"src": "hda", "id": "e39577a68c81d858"}, "input_type": "solexa", "options_type|output_type": "solexa", "options_type|force_quality_encoding": "ascii", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "e5c6fd44d073f013", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:14:35.894170", "create_time": "2024-09-23T13:14:23.752941", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-rk9rg", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/5/5/f/dataset_55f321b6-bd87-4682-824a-f51229081a9a.dat' solexa '/galaxy/server/database/objects/6/e/8/dataset_6e8bc424-4436-46a5-bbb7-64d0ea187602.dat' solexa ascii summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"ascii\", \"options_type_selector\": \"advanced\", \"output_type\": \"solexa\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"solexa\""}, "inputs": {"input_file": {"id": "e39577a68c81d858", "src": "hda", "uuid": "55f321b6-bd87-4682-824a-f51229081a9a"}}, "outputs": {"output_file": {"id": "5b274e5ec2ca21ae", "src": "hda", "uuid": "6e8bc424-4436-46a5-bbb7-64d0ea187602"}}, "output_collections": {}, "tool_stdout": "Groomed 2 solexa reads into solexa reads.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 solexa reads into solexa reads.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:14:25", "plugin": "core", "name": "start_epoch", "raw_value": "1727097265.0000000"}, {"title": "Job End Time", "value": "2024-09-23 13:14:25", "plugin": "core", "name": "end_epoch", "raw_value": "1727097265.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-32", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 32, "time_seconds": 32.82215476036072, "inputs": {"input_file": {"src": "hda", "id": "6f1141918821322a"}, "input_type": "solexa", "options_type|output_type": "solexa", "options_type|force_quality_encoding": "decimal", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "a650938ff37ae699", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:15:09.221289", "create_time": "2024-09-23T13:14:55.464288", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-sxfbh", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/d/a/6/dataset_da6d66d7-a900-4d59-9339-61ea23ec029e.dat' solexa '/galaxy/server/database/objects/7/a/8/dataset_7a83537b-11b5-4464-9396-dc5c9779994c.dat' solexa decimal summarize_input --fix-id", "traceback": null, "params": {"__input_ext": "\"fastq\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"decimal\", \"options_type_selector\": \"advanced\", \"output_type\": \"solexa\", \"summarize_input\": \"summarize_input\"}", "input_type": "\"solexa\""}, "inputs": {"input_file": {"id": "6f1141918821322a", "src": "hda", "uuid": "da6d66d7-a900-4d59-9339-61ea23ec029e"}}, "outputs": {"output_file": {"id": "0cad9bac291447c2", "src": "hda", "uuid": "7a83537b-11b5-4464-9396-dc5c9779994c"}}, "output_collections": {}, "tool_stdout": "Groomed 2 solexa reads into solexa reads.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 solexa reads into solexa reads.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "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": "2024-09-23 13:14:58", "plugin": "core", "name": "end_epoch", "raw_value": "1727097298.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:14:57", "plugin": "core", "name": "start_epoch", "raw_value": "1727097297.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-33", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 33, "time_seconds": 33.081300497055054, "inputs": {"input_file": {"src": "hda", "id": "96586eaff11d98c8"}, "input_type": "sanger", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "32a712ea8ae079d2", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:15:42.459179", "create_time": "2024-09-23T13:15:30.063607", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-cvt65", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/c/8/0/dataset_c80e26a9-58bc-4287-a736-d1eb9e926bce.dat' sanger.gz '/galaxy/server/database/objects/4/3/d/dataset_43da497c-f41c-42f0-9877-0e19b65467fa.dat' sanger ascii summarize_input", "traceback": null, "params": {"__input_ext": "\"fastq.gz\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "input_type": "\"sanger\""}, "inputs": {"input_file": {"id": "96586eaff11d98c8", "src": "hda", "uuid": "c80e26a9-58bc-4287-a736-d1eb9e926bce"}}, "outputs": {"output_file": {"id": "7cc0da2f475bb616", "src": "hda", "uuid": "43da497c-f41c-42f0-9877-0e19b65467fa"}}, "output_collections": {}, "tool_stdout": "Groomed 2 sanger.gz reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 sanger.gz reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: sanger, sanger.gz, sanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "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": "2024-09-23 13:15:31", "plugin": "core", "name": "end_epoch", "raw_value": "1727097331.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:15:31", "plugin": "core", "name": "start_epoch", "raw_value": "1727097331.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-34", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 34, "time_seconds": 25.67445945739746, "inputs": {"input_file": {"src": "hda", "id": "00ceb129d5865519"}, "input_type": "cssanger", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "2e416ed01d13ae5f", "state": "error", "exit_code": null, "update_time": "2024-09-23T13:16:08.450429", "create_time": "2024-09-23T13:16:03.315857", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-tmrhs", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/d/e/b/dataset_deb69f7d-fb95-4061-b65c-ff8c62fb783e.dat' cssanger.bz2 '/galaxy/server/database/objects/e/0/4/dataset_e043c9fc-efe8-4f74-a4af-b09713ad6881.dat' cssanger ascii summarize_input", "traceback": null, "params": {"__input_ext": "\"fastq.bz2\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "input_type": "\"cssanger\""}, "inputs": {"input_file": {"id": "00ceb129d5865519", "src": "hda", "uuid": "deb69f7d-fb95-4061-b65c-ff8c62fb783e"}}, "outputs": {"output_file": {"id": "c7371e849dcb6dbd", "src": "hda", "uuid": "e043c9fc-efe8-4f74-a4af-b09713ad6881"}}, "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/devteam/fastq_groomer/fastq_groomer/1.1.5, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "fastq_groomer/1.1.5-4", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 4, "time_seconds": 32.40282416343689, "inputs": {"input_file": {"src": "hda", "id": "bb0ee569d20f5f6f"}, "input_type": "cssanger", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "09edacbd04fc16f4", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:00:27.585878", "create_time": "2024-09-23T13:00:14.423702", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-xx6s8", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/f/6/e/dataset_f6ece6ff-4638-46cd-a3b7-15666d561c78.dat' cssanger '/galaxy/server/database/objects/b/0/e/dataset_b0e2aa11-b040-4a8f-88d3-5688a1e765eb.dat' cssanger ascii summarize_input", "traceback": null, "params": {"input_type": "\"cssanger\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "bb0ee569d20f5f6f", "src": "hda", "uuid": "f6ece6ff-4638-46cd-a3b7-15666d561c78"}}, "outputs": {"output_file": {"id": "d2fcdfe1ee2eaecf", "src": "hda", "uuid": "b0e2aa11-b040-4a8f-88d3-5688a1e765eb"}}, "output_collections": {}, "tool_stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 cssanger reads into cssanger reads.\nBased upon quality and sequence, the input data is valid for: cssanger, cssanger.gz, cssanger.bz2\nInput ASCII range: '!'(33) - '~'(126)\nInput decimal range: 0 - 93\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:00:16", "plugin": "core", "name": "start_epoch", "raw_value": "1727096416.0000000"}, {"title": "Job End Time", "value": "2024-09-23 13:00:16", "plugin": "core", "name": "end_epoch", "raw_value": "1727096416.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-5", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 5, "time_seconds": 33.15273904800415, "inputs": {"input_file": {"src": "hda", "id": "b8f747c82e08bb4e"}, "input_type": "illumina", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "18f54c2e60adeca1", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:01:00.751529", "create_time": "2024-09-23T13:00:48.189196", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-lzglh", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/2/5/8/dataset_2582dd27-75fc-4bec-a808-a028c86ab7d4.dat' illumina '/galaxy/server/database/objects/8/3/6/dataset_83639a54-fcdd-4289-815e-73ddfa54bf1a.dat' sanger ascii summarize_input", "traceback": null, "params": {"input_type": "\"illumina\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "b8f747c82e08bb4e", "src": "hda", "uuid": "2582dd27-75fc-4bec-a808-a028c86ab7d4"}}, "outputs": {"output_file": {"id": "80a9eb76f24a2903", "src": "hda", "uuid": "83639a54-fcdd-4289-815e-73ddfa54bf1a"}}, "output_collections": {}, "tool_stdout": "Groomed 2 illumina reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 illumina reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:00:50", "plugin": "core", "name": "start_epoch", "raw_value": "1727096450.0000000"}, {"title": "Job End Time", "value": "2024-09-23 13:00:50", "plugin": "core", "name": "end_epoch", "raw_value": "1727096450.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-6", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 6, "time_seconds": 32.32887363433838, "inputs": {"input_file": {"src": "hda", "id": "5579e0afcc587725"}, "input_type": "solexa", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "d1e4507abeaf9074", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:01:33.187773", "create_time": "2024-09-23T13:01:20.656130", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-ql56k", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/2/7/e/dataset_27e1ad84-d7d2-4005-9db3-9fdbe14bc2ff.dat' solexa '/galaxy/server/database/objects/2/1/b/dataset_21b14d85-48dd-45cc-b514-9d5c1c043d30.dat' sanger ascii summarize_input", "traceback": null, "params": {"input_type": "\"solexa\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "5579e0afcc587725", "src": "hda", "uuid": "27e1ad84-d7d2-4005-9db3-9fdbe14bc2ff"}}, "outputs": {"output_file": {"id": "d5a62abe1cd005d4", "src": "hda", "uuid": "21b14d85-48dd-45cc-b514-9d5c1c043d30"}}, "output_collections": {}, "tool_stdout": "Groomed 2 solexa reads into sanger reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 solexa reads into sanger reads.\nConverted between Solexa and PHRED scores.\nBased upon quality and sequence, the input data is valid for: solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: ';'(59) - '~'(126)\nInput decimal range: -5 - 62\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:01:22", "plugin": "core", "name": "start_epoch", "raw_value": "1727096482.0000000"}, {"title": "Job End Time", "value": "2024-09-23 13:01:22", "plugin": "core", "name": "end_epoch", "raw_value": "1727096482.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-7", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 7, "time_seconds": 32.290194272994995, "inputs": {"input_file": {"src": "hda", "id": "af045946503fce90"}, "input_type": "sanger", "options_type|options_type_selector": "basic"}, "job": {"model_class": "Job", "id": "431d179f1c8481cc", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:02:05.743260", "create_time": "2024-09-23T13:01:52.686329", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-g76sr", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/2/b/a/dataset_2ba13390-c3d2-4002-8d3a-e773d3a3ad83.dat' sanger '/galaxy/server/database/objects/f/8/6/dataset_f86e0890-fda3-4c3f-8dcc-e660acde5a88.dat' sanger ascii summarize_input", "traceback": null, "params": {"input_type": "\"sanger\"", "options_type": "{\"__current_case__\": 0, \"options_type_selector\": \"basic\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "af045946503fce90", "src": "hda", "uuid": "2ba13390-c3d2-4002-8d3a-e773d3a3ad83"}}, "outputs": {"output_file": {"id": "374937641cb6242d", "src": "hda", "uuid": "f86e0890-fda3-4c3f-8dcc-e660acde5a88"}}, "output_collections": {}, "tool_stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 31 - 93\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 sanger reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 31 - 93\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:01:54", "plugin": "core", "name": "start_epoch", "raw_value": "1727096514.0000000"}, {"title": "Job End Time", "value": "2024-09-23 13:01:54", "plugin": "core", "name": "end_epoch", "raw_value": "1727096514.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-8", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 8, "time_seconds": 31.455182552337646, "inputs": {"input_file": {"src": "hda", "id": "8968cffb028e4eba"}, "input_type": "illumina", "options_type|output_type": "illumina", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "13677f2b12ecd8d8", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:02:37.257039", "create_time": "2024-09-23T13:02:24.282739", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-7wfjk", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/2/b/1/dataset_2b17bf00-7e83-49e0-8d6a-cf67f894ef5c.dat' illumina '/galaxy/server/database/objects/d/2/3/dataset_d23de7aa-4aca-4ea2-934e-dfe4f867add8.dat' illumina None summarize_input --fix-id", "traceback": null, "params": {"input_type": "\"illumina\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"illumina\", \"summarize_input\": \"summarize_input\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "8968cffb028e4eba", "src": "hda", "uuid": "2b17bf00-7e83-49e0-8d6a-cf67f894ef5c"}}, "outputs": {"output_file": {"id": "8dfb5501d2079009", "src": "hda", "uuid": "d23de7aa-4aca-4ea2-934e-dfe4f867add8"}}, "output_collections": {}, "tool_stdout": "Groomed 2 illumina reads into illumina reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 illumina reads into illumina reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:02:26", "plugin": "core", "name": "start_epoch", "raw_value": "1727096546.0000000"}, {"title": "Job End Time", "value": "2024-09-23 13:02:26", "plugin": "core", "name": "end_epoch", "raw_value": "1727096546.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "fastq_groomer/1.1.5-9", "has_data": true, "data": {"tool_id": "fastq_groomer", "tool_version": "1.1.5", "test_index": 9, "time_seconds": 32.26587462425232, "inputs": {"input_file": {"src": "hda", "id": "e609d34f51e3c720"}, "input_type": "illumina", "options_type|output_type": "sanger", "options_type|force_quality_encoding": "None", "options_type|summarize_input": "summarize_input", "options_type|options_type_selector": "advanced"}, "job": {"model_class": "Job", "id": "7956f1cdb5e2e625", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T13:03:09.732703", "create_time": "2024-09-23T13:02:56.734180", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "history_id": "947bb6702479ed20", "external_id": "gxy-n8r22", "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/1/a/2/dataset_1a24599c-0492-466b-91b7-192f8ee0f7a7.dat' illumina '/galaxy/server/database/objects/3/d/7/dataset_3d73f1f8-4c64-46d5-aa7a-09e764bc81ae.dat' sanger None summarize_input --fix-id", "traceback": null, "params": {"input_type": "\"illumina\"", "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastq\""}, "inputs": {"input_file": {"id": "e609d34f51e3c720", "src": "hda", "uuid": "1a24599c-0492-466b-91b7-192f8ee0f7a7"}}, "outputs": {"output_file": {"id": "9e9bef3212786702", "src": "hda", "uuid": "3d73f1f8-4c64-46d5-aa7a-09e764bc81ae"}}, "output_collections": {}, "tool_stdout": "Groomed 2 illumina reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Groomed 2 illumina reads into sanger reads.\nBased upon quality and sequence, the input data is valid for: illumina, illumina.gz, illumina.bz2, solexa, solexa.gz, solexa.bz2, sanger, sanger.gz, sanger.bz2\nInput ASCII range: '@'(64) - '~'(126)\nInput decimal range: 0 - 62\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 13:02:58", "plugin": "core", "name": "start_epoch", "raw_value": "1727096578.0000000"}, {"title": "Job End Time", "value": "2024-09-23 13:02:58", "plugin": "core", "name": "end_epoch", "raw_value": "1727096578.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "ncbi_acc_download/0.2.8+galaxy0-0", "has_data": true, "data": {"tool_id": "ncbi_acc_download", "tool_version": "0.2.8+galaxy0", "test_index": 0, "time_seconds": 104.00350069999695, "inputs": {"query_source|accession_file": {"src": "hda", "id": "947bb6702479ed20"}, "query_source|select": "accession_file", "molecule|format": "fasta", "molecule|select": "nucleotide"}, "job": {"model_class": "Job", "id": "2de01d98ed94e7fa", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T12:53:35.079619", "create_time": "2024-09-23T12:52:43.910206", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0", "history_id": "947bb6702479ed20", "external_id": "gxy-l4vcx", "command_line": "{ grep -v \"^[ \\t]*$\" /galaxy/server/database/objects/0/a/b/dataset_0abe3e40-eab8-4012-a718-02acf6258494.dat > accessions || { echo \"No accession numbers in input. 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Aborting.\" 1>&2; exit 1; } } && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'genbank' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "traceback": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ignore_failed": "\"0\"", "range": null, "molecule": "{\"__current_case__\": 0, \"format\": \"genbank\", \"select\": \"nucleotide\"}", "query_source": "{\"__current_case__\": 0, \"accession_file\": {\"values\": [{\"id\": 5, \"src\": \"hda\"}]}, \"select\": \"accession_file\"}"}, "inputs": {"query_source|accession_file": {"id": "ca1a7ff542832f6a", "src": "hda", "uuid": "4f3d96de-e7da-41b9-b666-90dcad0706f0"}}, "outputs": {"__new_primary_file_output|CP021680__": {"id": "dc350d755d4846e0", "src": "hda", "uuid": "ecfe5488-8b24-4e39-bd66-d20cb58666e7"}, "__new_primary_file_output|CP011064__": {"id": "fa37247bbcc1ec5a", "src": "hda", "uuid": "4cb597bf-381f-4e58-8ec4-ad4fdece9caa"}, "error_log": {"id": "2079e80a52b9f098", "src": "hda", "uuid": "8024b187-6bf1-4403-8c11-992655c39daf"}}, "output_collections": {"output": {"id": "2de01d98ed94e7fa", "src": "hdca"}}, "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": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}, {"title": "Job End Time", "value": "2024-09-23 12:54:02", "plugin": "core", "name": "end_epoch", "raw_value": "1727096042.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 12:53:56", "plugin": "core", "name": "start_epoch", "raw_value": "1727096036.0000000"}, {"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": "ncbi_acc_download/0.2.8+galaxy0-10", "has_data": true, "data": {"tool_id": "ncbi_acc_download", "tool_version": "0.2.8+galaxy0", "test_index": 10, "time_seconds": 15.901856184005737, "inputs": {"query_source|accession_list": "NC_006666", "query_source|select": "accession_list", "molecule|format": "genbank", "molecule|select": "nucleotide", "range": "1697:2764"}, "job": {"model_class": "Job", "id": "327271a847b6aeda", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T12:57:36.406580", "create_time": "2024-09-23T12:57:21.621457", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0", "history_id": "947bb6702479ed20", "external_id": "gxy-kp52v", "command_line": "echo 'NC_006666' | sed -r 's/(\\,|__cn__)/\\n/g' | grep -v \"^[ \\t]*$\" > accessions && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'genbank' --extended-validation all --range 1697:2764 ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "traceback": null, "params": {"query_source": "{\"__current_case__\": 1, \"accession_list\": \"NC_006666\", \"select\": \"accession_list\"}", "molecule": "{\"__current_case__\": 0, \"format\": \"genbank\", \"select\": \"nucleotide\"}", "range": "\"1697:2764\"", "ignore_failed": "\"0\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"data\""}, "inputs": {}, "outputs": {"__new_primary_file_output|NC_006666__": {"id": "5fc883da7dbbb2f2", "src": "hda", "uuid": "580d9f66-6480-4325-9233-ffe1c23226e6"}, "error_log": {"id": "13677f2b12ecd8d8", "src": "hda", "uuid": "385a5718-fb7c-4cce-8272-0e0773fedcdb"}}, "output_collections": {"output": {"id": "b4ffb4ffa6e15902", "src": "hdca"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 12:57:23", "plugin": "core", "name": "start_epoch", "raw_value": "1727096243.0000000"}, {"title": "Job End Time", "value": "2024-09-23 12:57:26", "plugin": "core", "name": "end_epoch", "raw_value": "1727096246.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}]}, "status": "success"}}, {"id": "ncbi_acc_download/0.2.8+galaxy0-2", "has_data": true, "data": {"tool_id": "ncbi_acc_download", "tool_version": "0.2.8+galaxy0", "test_index": 2, "time_seconds": 38.51488637924194, "inputs": {"query_source|accession_file": {"src": "hda", "id": "0ebe743b0a6a67ba"}, "query_source|select": "accession_file", "molecule|format": "gff3", "molecule|select": "nucleotide"}, "job": {"model_class": "Job", "id": "2079e80a52b9f098", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T12:54:50.998464", "create_time": "2024-09-23T12:54:32.138738", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0", "history_id": "947bb6702479ed20", "external_id": "gxy-krzd7", "command_line": "{ grep -v \"^[ \\t]*$\" /galaxy/server/database/objects/4/b/7/dataset_4b7bae7f-a7fa-4bf6-b5cf-5233a473aefe.dat > accessions || { echo \"No accession numbers in input. Aborting.\" 1>&2; exit 1; } } && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'gff3' ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "traceback": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ignore_failed": "\"0\"", "range": null, "molecule": "{\"__current_case__\": 0, \"format\": \"gff3\", \"select\": \"nucleotide\"}", "query_source": "{\"__current_case__\": 0, \"accession_file\": {\"values\": [{\"id\": 9, \"src\": \"hda\"}]}, \"select\": \"accession_file\"}"}, "inputs": {"query_source|accession_file": {"id": "0ebe743b0a6a67ba", "src": "hda", "uuid": "4b7bae7f-a7fa-4bf6-b5cf-5233a473aefe"}}, "outputs": {"__new_primary_file_output|CP021680__": {"id": "b849e135bbda4f49", "src": "hda", "uuid": "0dfb794e-2932-4a5c-8e40-08b303a83233"}, "__new_primary_file_output|CP011064__": {"id": "b4ffb4ffa6e15902", "src": "hda", "uuid": "cdc90f88-9a20-44d8-8315-7ea3e22fc56e"}, "error_log": {"id": "09e002d77c54e484", "src": "hda", "uuid": "5322d6ba-2230-45a9-81ea-7b8dee37ac7f"}}, "output_collections": {"output": {"id": "72098edaf93336c2", "src": "hdca"}}, "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": "8 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "8.0000000"}, {"title": "Job End Time", "value": "2024-09-23 12:54:41", "plugin": "core", "name": "end_epoch", "raw_value": "1727096081.0000000"}, {"title": "Job Start Time", "value": "2024-09-23 12:54:33", "plugin": "core", "name": "start_epoch", "raw_value": "1727096073.0000000"}, {"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": "ncbi_acc_download/0.2.8+galaxy0-3", "has_data": true, "data": {"tool_id": "ncbi_acc_download", "tool_version": "0.2.8+galaxy0", "test_index": 3, "time_seconds": 38.48298382759094, "inputs": {"query_source|accession_file": {"src": "hda", "id": "0f809caf69144a2f"}, "query_source|select": "accession_file", "molecule|format": "featuretable", "molecule|select": "nucleotide"}, "job": {"model_class": "Job", "id": "dc350d755d4846e0", "state": "ok", "exit_code": 0, "update_time": "2024-09-23T12:55:29.731549", "create_time": "2024-09-23T12:55:11.666180", "galaxy_version": "23.1", "command_version": null, "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0", "history_id": "947bb6702479ed20", "external_id": "gxy-7pptn", "command_line": "{ grep -v \"^[ \\t]*$\" /galaxy/server/database/objects/7/b/c/dataset_7bc4dd59-34e1-4de4-b02c-dfecc7f42e9e.dat > accessions || { echo \"No accession numbers in input. Aborting.\" 1>&2; exit 1; } } && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'featuretable' ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "traceback": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ignore_failed": "\"0\"", "range": null, "molecule": "{\"__current_case__\": 0, \"format\": \"featuretable\", \"select\": \"nucleotide\"}", "query_source": "{\"__current_case__\": 0, \"accession_file\": {\"values\": [{\"id\": 13, \"src\": \"hda\"}]}, \"select\": \"accession_file\"}"}, "inputs": 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../error.log >&2);", "traceback": null, "params": {"query_source": "{\"__current_case__\": 1, \"accession_list\": \"CP011064,CP0XXXXX,CP021680\", \"select\": \"accession_list\"}", "molecule": "{\"__current_case__\": 0, \"format\": \"fasta\", \"select\": \"nucleotide\"}", "range": null, "ignore_failed": "\"1\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"data\""}, "inputs": {}, "outputs": {"error_log": {"id": "748026805d8e73fb", "src": "hda", "uuid": "c33703c3-1bd6-455d-8ecc-fe2cc6fbe6f6"}, "failed_accessions": {"id": "7956cb04120de21b", "src": "hda", "uuid": "26b1ff64-66ad-4931-b8a6-00cf2583cc62"}, "__new_primary_file_output|CP011064__": {"id": "ac4b0d61c0d502ff", "src": "hda", "uuid": "ac657714-ac2d-46d7-a189-0367ca249e47"}, "__new_primary_file_output|CP021680__": {"id": "df3c8fdfb989b284", "src": "hda", "uuid": "249ec4a4-d527-4697-9cfd-7f6315784686"}}, "output_collections": {"output": {"id": "2079e80a52b9f098", "src": 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