From f501fdbae7313419a130f3d4b7c1bd6aaa1f19a1 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Thu, 26 Oct 2023 15:07:29 +0000 Subject: [PATCH] Updating anvil-production README for gtests-prod-2023-10-26-12-27-1 --- reports/anvil-production/README.md | 2 +- .../anvil-production/tool-tests/chunks.json | 10 +- .../gtests-prod-2023-10-26-12-27-1/chunk.json | 7 + .../gtests-prod-2023-10-26-12-27-1/chunk.txt | 15 + .../gtests-prod-2023-10-26-12-27-1/jobs.txt | 199 +++++ .../results.html | 291 ++++++++ .../results.json | 1 + .../results.xunit | 688 ++++++++++++++++++ .../gtests-prod-2023-10-26-12-27-1/tools.yml | 92 +++ 9 files changed, 1299 insertions(+), 6 deletions(-) create mode 100644 reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/chunk.json create mode 100644 reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/chunk.txt create mode 100644 reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/jobs.txt create mode 100644 reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/results.html create mode 100644 reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/results.json create mode 100644 reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/results.xunit create mode 100644 reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/tools.yml diff --git a/reports/anvil-production/README.md b/reports/anvil-production/README.md index 5b13a31de..98d037558 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 Oct 23 00:43:46 2023Mon Oct 16 00:43:57 2023
1ToolsetMon Oct 23 12:45:56 2023Mon Oct 16 12:47:48 2023
2ToolsetTue Oct 24 00:43:01 2023Tue Oct 17 00:42:55 2023
3ToolsetTue Oct 24 12:45:08 2023Tue Oct 17 12:46:22 2023
4ToolsetWed Oct 25 00:42:17 2023Wed Oct 18 00:42:46 2023
5ToolsetWed Oct 25 12:44:39 2023Wed Oct 18 12:46:09 2023
6ToolsetThu Oct 26 00:41:20 2023Thu Oct 19 00:43:39 2023
7ToolsetThu Oct 19 12:46:05 2023Thu Oct 12 12:46:26 2023
8ToolsetFri Oct 20 00:42:08 2023Fri Oct 13 00:43:24 2023
9ToolsetFri Oct 20 12:44:37 2023Fri Oct 13 12:45:38 2023
10ToolsetSat Oct 21 00:41:52 2023Sat Oct 14 00:41:31 2023
11ToolsetSat Oct 21 12:43:13 2023Sat Oct 14 12:42:02 2023
12ToolsetSun Oct 22 00:45:03 2023Sun Oct 15 00:45:27 2023
13ToolsetSun Oct 22 12:42:28 2023Sun Oct 15 12:42:34 2023
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Oct 23 00:43:46 2023Mon Oct 16 00:43:57 2023
1ToolsetMon Oct 23 12:45:56 2023Mon Oct 16 12:47:48 2023
2ToolsetTue Oct 24 00:43:01 2023Tue Oct 17 00:42:55 2023
3ToolsetTue Oct 24 12:45:08 2023Tue Oct 17 12:46:22 2023
4ToolsetWed Oct 25 00:42:17 2023Wed Oct 18 00:42:46 2023
5ToolsetWed Oct 25 12:44:39 2023Wed Oct 18 12:46:09 2023
6ToolsetThu Oct 26 00:41:20 2023Thu Oct 19 00:43:39 2023
7ToolsetThu Oct 26 12:44:42 2023Thu Oct 19 12:46:05 2023
8ToolsetFri Oct 20 00:42:08 2023Fri Oct 13 00:43:24 2023
9ToolsetFri Oct 20 12:44:37 2023Fri Oct 13 12:45:38 2023
10ToolsetSat Oct 21 00:41:52 2023Sat Oct 14 00:41:31 2023
11ToolsetSat Oct 21 12:43:13 2023Sat Oct 14 12:42:02 2023
12ToolsetSun Oct 22 00:45:03 2023Sun Oct 15 00:45:27 2023
13ToolsetSun Oct 22 12:42:28 2023Sun Oct 15 12:42:34 2023
diff --git a/reports/anvil-production/tool-tests/chunks.json b/reports/anvil-production/tool-tests/chunks.json index b09093fe3..9d8766aa6 100644 --- a/reports/anvil-production/tool-tests/chunks.json +++ b/reports/anvil-production/tool-tests/chunks.json @@ -91,10 +91,10 @@ "date2": "Mon Oct 16 00:43:57 2023" }, "7": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-19-12-28-1/results.html", - "date1": "Thu Oct 19 12:46:05 2023", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-19-12-28-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-12-12-28-1/results.html", - "date2": "Thu Oct 12 12:46:26 2023" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/results.html", + "date1": "Thu Oct 26 12:44:42 2023", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-19-12-28-1/results.html", + "date2": "Thu Oct 19 12:46:05 2023" } } \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/chunk.json b/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/chunk.json new file mode 100644 index 000000000..2b52d2601 --- /dev/null +++ b/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/chunk.json @@ -0,0 +1,7 @@ +{ + "7": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/results.html", + "date1": "Thu Oct 26 12:44:42 2023", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/chunk.txt b/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/chunk.txt new file mode 100644 index 000000000..07a0e8883 --- /dev/null +++ b/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/chunk.txt @@ -0,0 +1,15 @@ +-t query_tabular --tool-version 83069b38aa85 +-t column_remove_by_header --tool-version 372967836e98 +-t multiqc --tool-version 75c93c70d094 +-t samtools_phase --tool-version b5c3b1856370 +-t samtools_mpileup --tool-version fa7ad9b89f4a +-t bcftools_query_list_samples --tool-version ed4ea9de1791 +-t bcftools_isec --tool-version 02f349bdbf96 +-t vcfannotate --tool-version 01e0321aca98 +-t vcfrandomsample --tool-version 6257ee3b50d3 +-t nanoplot --tool-version edbb6c5028f5 +-t poretools_extract --tool-version 7e4f1ed70187 +-t deeptools_plot_fingerprint --tool-version 2da482e408b8 +-t lofreq_call --tool-version e1461b5c52a0 +-t ivar_getmasked --tool-version 2cf4a1cafc16 +-t jbrowse --tool-version 4542035c1075 diff --git a/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/jobs.txt b/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/jobs.txt new file mode 100644 index 000000000..5f0274091 --- /dev/null +++ b/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/jobs.txt @@ -0,0 +1,199 @@ +936bbdad97015d85 ok 2023-10-26T15:07:23.009177 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 +876cc9de8310081b ok 2023-10-26T15:05:23.157135 upload1 +5e3ce93f9640e07c ok 2023-10-26T15:05:13.450331 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2023-10-26T14:00:56.701597 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4 +aed1dd285d3a92db ok 2023-10-26T13:58:50.547764 upload1 +c4c146f740b4d349 ok 2023-10-26T13:58:50.212878 upload1 +931816e04032d6bf ok 2023-10-26T13:58:39.250919 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4 +2e36d71d4190699e ok 2023-10-26T13:56:37.100870 upload1 +87e82e1fbd05f3e5 ok 2023-10-26T13:56:36.634884 upload1 +f422c15e29477b69 ok 2023-10-26T13:56:25.804170 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4 +d579590a12a92696 ok 2023-10-26T13:54:21.365706 upload1 +3993b83cedc80c32 ok 2023-10-26T13:54:21.129794 upload1 +4e1e655f8f24586d ok 2023-10-26T13:54:10.425939 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4 +5408b1f2c036bc8b ok 2023-10-26T13:52:01.667483 upload1 +845e2d56717d34ab ok 2023-10-26T13:52:01.366213 upload1 +ae1396693019fa0a ok 2023-10-26T13:51:50.058692 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upload1 +18923b9324b83db6 ok 2023-10-26T12:51:58.566499 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +e3e0a50be7ada402 ok 2023-10-26T12:49:57.928614 upload1 +039be4ea35941c03 ok 2023-10-26T12:49:47.384420 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +43eedd38907c81b8 ok 2023-10-26T12:47:51.980220 upload1 +14fc6761762314fb ok 2023-10-26T12:47:51.968663 upload1 +d9b33f37b24cefc3 ok 2023-10-26T12:47:39.194962 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 +5e8afed7230bd521 ok 2023-10-26T12:45:27.540031 upload1 +c71426eac153eb4f ok 2023-10-26T12:45:27.514515 upload1 diff --git a/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/results.html b/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/results.html new file mode 100644 index 000000000..3c2f7059f --- /dev/null +++ b/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/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/gtests-prod-2023-10-26-12-27-1/results.json b/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/results.json new file mode 100644 index 000000000..b0bf13a84 --- /dev/null +++ b/reports/anvil-production/tool-tests/gtests-prod-2023-10-26-12-27-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 55, "errors": 0, "failures": 5, "skips": 0}, "tests": [{"id": "bcftools_isec/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_isec", "tool_version": "1.10", "test_index": 0, "time_seconds": 128.60520887374878, "inputs": {"input_files": [{"src": "hda", "id": "f1a82b8d22bc9b74"}, {"src": "hda", "id": "7454aa129ae8c898"}], "sec_default|nfiles": "=2", "output_type": "v"}, "job": {"model_class": "Job", "id": "cf7ff2ac77061d35", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:05:23.648427", "create_time": "2023-10-26T14:03:26.612735", "galaxy_version": "21.09", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_isec/bcftools_isec/1.10", "history_id": "c71426eac153eb4f", "external_id": "gxy-p9l5x", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/b/f/1/dataset_bf114d04-b9da-455c-a726-1315720d3b2e.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/2/d/0/dataset_2d0fc3d9-2091-4021-99de-9e2118a544fb.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools isec --nfiles \"=2\" --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/4/2/d/dataset_42dd45a6-e178-49cf-a681-eb43db3336c4.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"complement\": \"false\", \"nfiles\": \"=2\", \"prefix\": \"false\", \"write\": null}", "sec_restrict": "{\"apply_filters\": \"\", \"collapse\": null, \"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}"}, "inputs": {"input_files": {"id": "f1a82b8d22bc9b74", "src": "hda", "uuid": "bf114d04-b9da-455c-a726-1315720d3b2e"}, "input_files1": {"id": "f1a82b8d22bc9b74", "src": "hda", "uuid": "bf114d04-b9da-455c-a726-1315720d3b2e"}, "input_files2": {"id": "7454aa129ae8c898", "src": "hda", "uuid": "2d0fc3d9-2091-4021-99de-9e2118a544fb"}}, "outputs": {"output_file": {"id": "02b5b5f70065f1bb", "src": "hda", "uuid": "42dd45a6-e178-49cf-a681-eb43db3336c4"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "Note: -w option not given, printing list of sites...\n", "stderr": "\nNote: -w option not given, printing list of sites...\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-26 14:05:15", "plugin": "core", "name": "end_epoch", "raw_value": "1698329115.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:05:14", "plugin": "core", "name": "start_epoch", "raw_value": "1698329114.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_query_list_samples/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_query_list_samples", "tool_version": "1.10", "test_index": 0, "time_seconds": 135.986492395401, "inputs": {"input_file": {"src": "hda", "id": "ee37e2b0e7bd19e7"}}, "job": {"model_class": "Job", "id": "12b7da2e48f38389", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:03:14.044091", "create_time": "2023-10-26T14:01:07.701767", "galaxy_version": "21.09", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query_list_samples/bcftools_query_list_samples/1.10", "history_id": "c71426eac153eb4f", "external_id": "gxy-kb7hg", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/d/4/e/dataset_d4e4a1c3-dd1b-4c5b-885c-c662ba1dbc5d.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools query --list-samples input.vcf.gz | tee /galaxy/server/database/objects/8/6/c/dataset_86c1d6ee-bc15-4c3d-918c-b71469800481.dat | tr '\\n' ','", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input_file": {"id": "ee37e2b0e7bd19e7", "src": "hda", "uuid": "d4e4a1c3-dd1b-4c5b-885c-c662ba1dbc5d"}}, "outputs": {"output_file": {"id": "c4f0d7e6ba75d6a7", "src": "hda", "uuid": "86c1d6ee-bc15-4c3d-918c-b71469800481"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "C,D,", "job_stderr": "", "stderr": "", "stdout": "\nC,D,", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-26 14:03:04", "plugin": "core", "name": "end_epoch", "raw_value": "1698328984.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:03:04", "plugin": "core", "name": "start_epoch", "raw_value": "1698328984.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "column_remove_by_header/0.0.1-0", "has_data": true, "data": {"tool_id": "column_remove_by_header", "tool_version": "0.0.1", "test_index": 0, "time_seconds": 133.63202047348022, "inputs": {"input_tabular": {"src": "hda", "id": "06f7506129634457"}, "headers_0|name": "a", "keep_columns": false, "strip_characters": "#"}, "job": {"model_class": "Job", "id": "06f7506129634457", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:14:01.554668", "create_time": "2023-10-26T13:11:58.330342", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1", "history_id": "c71426eac153eb4f", "external_id": "gxy-vhfxm", "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/372967836e98/column_remove_by_header/column_remove_by_header.py' '/galaxy/server/database/objects/e/f/4/dataset_ef454a3a-842a-438e-8bc5-8d4df57daa24.dat' '/galaxy/server/database/objects/0/b/3/dataset_0b39d6b6-212a-4234-8dde-b46c989a7ccc.dat' '\t' '' '#' 'a'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "strip_characters": "\"#\"", "keep_columns": "\"false\"", "headers": "[{\"__index__\": 0, \"name\": \"a\"}]"}, "inputs": {"input_tabular": {"id": "06f7506129634457", "src": "hda", "uuid": "ef454a3a-842a-438e-8bc5-8d4df57daa24"}}, "outputs": {"output_tabular": {"id": "c31fa5d450463bcc", "src": "hda", "uuid": "0b39d6b6-212a-4234-8dde-b46c989a7ccc"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Kept 3 of 4 columns.\n", "job_stderr": "", "stderr": "", "stdout": "\nKept 3 of 4 columns.\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": "2023-10-26 13:13:50", "plugin": "core", "name": "end_epoch", "raw_value": "1698326030.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:13:50", "plugin": "core", "name": "start_epoch", "raw_value": "1698326030.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "column_remove_by_header/0.0.1-1", "has_data": true, "data": {"tool_id": "column_remove_by_header", "tool_version": "0.0.1", "test_index": 1, "time_seconds": 130.41462540626526, "inputs": {"input_tabular": {"src": "hda", "id": "689ec3f3e4a5cd20"}, "headers_0|name": "KEY", "headers_1|name": "a", "keep_columns": true, "strip_characters": "#"}, "job": {"model_class": "Job", "id": "689ec3f3e4a5cd20", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:16:12.026191", "create_time": "2023-10-26T13:14:10.960575", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1", "history_id": "c71426eac153eb4f", "external_id": "gxy-rdz5l", "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/372967836e98/column_remove_by_header/column_remove_by_header.py' '/galaxy/server/database/objects/d/0/0/dataset_d003c422-2523-4c70-b2e0-b8dc299c4a1b.dat' '/galaxy/server/database/objects/d/3/4/dataset_d34c6718-d4ee-4aa3-b079-2810dd9fefaa.dat' '\t' '--keep' '#' 'KEY' 'a'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "strip_characters": "\"#\"", "keep_columns": "\"true\"", "headers": "[{\"__index__\": 0, \"name\": \"KEY\"}, {\"__index__\": 1, \"name\": \"a\"}]"}, "inputs": {"input_tabular": {"id": "689ec3f3e4a5cd20", "src": "hda", "uuid": "d003c422-2523-4c70-b2e0-b8dc299c4a1b"}}, "outputs": {"output_tabular": {"id": "d7384499ec7fb97a", "src": "hda", "uuid": "d34c6718-d4ee-4aa3-b079-2810dd9fefaa"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "Kept 2 of 4 columns.\n", "job_stderr": "", "stderr": "", "stdout": "\nKept 2 of 4 columns.\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": "2023-10-26 13:16:02", "plugin": "core", "name": "end_epoch", "raw_value": "1698326162.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:16:02", "plugin": "core", "name": "start_epoch", "raw_value": "1698326162.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "deeptools_plot_fingerprint/3.3.2.0.0-0", "has_data": true, "data": {"tool_id": "deeptools_plot_fingerprint", "tool_version": "3.3.2.0.0", "test_index": 0, "time_seconds": 160.78829884529114, "inputs": {"multibam_conditional|bamfiles": [{"src": "hda", "id": "235048ad61855ae3"}, {"src": "hda", "id": "235048ad61855ae3"}], "advancedOpt|showAdvancedOpt": "no", "output|showOutputSettings": "no"}, "job": {"model_class": "Job", "id": "a2d29193c8d1ced7", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:25:29.311818", "create_time": "2023-10-26T14:22:59.028696", "galaxy_version": "21.09", "command_version": "plotFingerprint 3.3.2", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0", "history_id": "c71426eac153eb4f", "external_id": "gxy-js6b8", "command_line": "ln -s '/galaxy/server/database/objects/2/a/a/dataset_2aadd58c-ab20-4a8f-8aac-779bd433b444.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/7/c/f/metadata_7cf34d73-e148-43f3-a952-9ec21147164c.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/2/a/a/dataset_2aadd58c-ab20-4a8f-8aac-779bd433b444.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/7/c/f/metadata_7cf34d73-e148-43f3-a952-9ec21147164c.dat' './1.bam.bai' && plotFingerprint --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bamfiles '0.bam' '1.bam' --labels 'bowtie2 test1.bam' 'bowtie2 test1.bam' --plotFile /galaxy/server/database/objects/5/a/e/dataset_5ae4a574-e63f-4453-bfc2-fbbe209e65e0.dat --plotFileFormat 'png'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output": "{\"__current_case__\": 0, \"showOutputSettings\": \"no\"}", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "region": "\"\"", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibam_conditional": "{\"__current_case__\": 0, \"bamfiles\": {\"values\": [{\"id\": 250, \"src\": \"hda\"}, {\"id\": 250, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}"}, "inputs": {"bamfiles": {"id": "235048ad61855ae3", "src": "hda", "uuid": "2aadd58c-ab20-4a8f-8aac-779bd433b444"}, "bamfiles1": {"id": "235048ad61855ae3", "src": "hda", "uuid": "2aadd58c-ab20-4a8f-8aac-779bd433b444"}, "bamfiles2": {"id": "235048ad61855ae3", "src": "hda", "uuid": "2aadd58c-ab20-4a8f-8aac-779bd433b444"}}, "outputs": {"outFileName": {"id": "66e1550ebbd48976", "src": "hda", "uuid": "5ae4a574-e63f-4453-bfc2-fbbe209e65e0"}}, "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": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2023-10-26 14:25:13", "plugin": "core", "name": "end_epoch", "raw_value": "1698330313.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:25:08", "plugin": "core", "name": "start_epoch", "raw_value": "1698330308.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "deeptools_plot_fingerprint/3.3.2.0.0-1", "has_data": true, "data": {"tool_id": "deeptools_plot_fingerprint", "tool_version": "3.3.2.0.0", "test_index": 1, "time_seconds": 153.70972418785095, "inputs": {"multibam_conditional|bamfiles": [{"src": "hda", "id": "1ebcdcca19a97754"}, {"src": "hda", "id": "1ebcdcca19a97754"}], "advancedOpt|plotTitle": "Test Fingerprint Plot", "advancedOpt|showAdvancedOpt": "yes", "output|saveRawCounts": true, "output|saveQualityMetrics": true, "output|JSDsample": {"src": "hda", "id": "1ebcdcca19a97754"}, "output|showOutputSettings": "yes"}, "job": {"model_class": "Job", "id": "1dcaa144d023bea5", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:28:02.275451", "create_time": "2023-10-26T14:25:41.218168", "galaxy_version": "21.09", "command_version": "plotFingerprint 3.3.2", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0", "history_id": "c71426eac153eb4f", "external_id": "gxy-mq2jm", "command_line": "ln -s '/galaxy/server/database/objects/6/a/3/dataset_6a3a6929-dad6-44a1-834c-c387dc48257d.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/3/4/4/metadata_344b8efc-624c-4810-8937-a7c410b96d6d.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/6/a/3/dataset_6a3a6929-dad6-44a1-834c-c387dc48257d.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/3/4/4/metadata_344b8efc-624c-4810-8937-a7c410b96d6d.dat' './1.bam.bai' && plotFingerprint --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bamfiles '0.bam' '1.bam' --labels 'bowtie2 test1.bam' 'bowtie2 test1.bam' --plotFile /galaxy/server/database/objects/d/e/6/dataset_de695b48-e492-45c6-b2b5-801edf046fee.dat --plotFileFormat png --outRawCounts '/galaxy/server/database/objects/2/4/2/dataset_242eea07-0574-4d3b-bbc9-505eaf9e708d.dat' --outQualityMetrics '/galaxy/server/database/objects/d/8/2/dataset_d82614dd-f492-4cba-8172-221a3c742c62.dat' --JSDsample '0.bam' --binSize '500' --numberOfSamples '100000' --plotTitle 'Test Fingerprint Plot' --minMappingQuality '1'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output": "{\"JSDsample\": {\"values\": [{\"id\": 253, \"src\": \"hda\"}]}, \"__current_case__\": 1, \"outFileFormat\": \"png\", \"saveQualityMetrics\": \"true\", \"saveRawCounts\": \"true\", \"showOutputSettings\": \"yes\"}", "advancedOpt": "{\"__current_case__\": 1, \"binSize\": \"500\", \"blackListFileName\": null, \"centerReads\": \"false\", \"doExtendCustom\": {\"__current_case__\": 0, \"doExtend\": \"no\"}, \"ignoreDuplicates\": \"false\", \"maxFragmentLength\": \"0\", \"minFragmentLength\": \"0\", \"minMappingQuality\": \"1\", \"numberOfSamples\": \"100000\", \"plotTitle\": \"Test Fingerprint Plot\", \"samFlagExclude\": \"\", \"samFlagInclude\": \"\", \"showAdvancedOpt\": \"yes\", \"skipZeros\": \"false\"}", "region": "\"\"", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibam_conditional": "{\"__current_case__\": 0, \"bamfiles\": {\"values\": [{\"id\": 253, \"src\": \"hda\"}, {\"id\": 253, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}"}, "inputs": {"bamfiles": {"id": "1ebcdcca19a97754", "src": "hda", "uuid": "6a3a6929-dad6-44a1-834c-c387dc48257d"}, "bamfiles1": {"id": "1ebcdcca19a97754", "src": "hda", "uuid": "6a3a6929-dad6-44a1-834c-c387dc48257d"}, "bamfiles2": {"id": "1ebcdcca19a97754", "src": "hda", "uuid": "6a3a6929-dad6-44a1-834c-c387dc48257d"}, "JSDsample": {"id": "1ebcdcca19a97754", "src": "hda", "uuid": "6a3a6929-dad6-44a1-834c-c387dc48257d"}}, "outputs": {"outFileName": {"id": "16700b0159c7ef03", "src": "hda", "uuid": "de695b48-e492-45c6-b2b5-801edf046fee"}, "outFileRawCounts": {"id": "a7a725250cca0157", "src": "hda", "uuid": "242eea07-0574-4d3b-bbc9-505eaf9e708d"}, "outFileQualityMetrics": {"id": "7310e79effef0a24", "src": "hda", "uuid": "d82614dd-f492-4cba-8172-221a3c742c62"}}, "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": "24 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "24.0000000"}, {"title": "Job End Time", "value": "2023-10-26 14:27:52", "plugin": "core", "name": "end_epoch", "raw_value": "1698330472.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:27:28", "plugin": "core", "name": "start_epoch", "raw_value": "1698330448.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "ivar_getmasked/1.2.2+galaxy0-0", "has_data": true, "data": {"tool_id": "ivar_getmasked", "tool_version": "1.2.2+galaxy0", "test_index": 0, "time_seconds": 137.3169765472412, "inputs": {"filtered_tsv": {"src": "hda", "id": "94d0ad32bacf6f6e"}, "primers_bed": {"src": "hda", "id": "26b128c199b1cf27"}, "primers_tsv": {"src": "hda", "id": "7b481a71741f4254"}}, "job": {"model_class": "Job", "id": "860cc653b8ea4f6e", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:41:47.581748", "create_time": "2023-10-26T14:39:45.940270", "galaxy_version": "21.09", "command_version": "iVar version 1.2.2", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_getmasked/ivar_getmasked/1.2.2+galaxy0", "history_id": "c71426eac153eb4f", "external_id": "gxy-kkztr", "command_line": "ivar getmasked -i '/galaxy/server/database/objects/6/8/5/dataset_6852fcfe-8419-4730-b8fa-4993250b5f75.dat' -b '/galaxy/server/database/objects/0/9/d/dataset_09d1c9df-e8dc-4ff8-ab94-214a160c2947.dat' -f '/galaxy/server/database/objects/1/d/9/dataset_1d90e1d4-8a03-40f4-813c-02d41118e0e8.dat' -p masked_primers", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"filtered_tsv": {"id": "94d0ad32bacf6f6e", "src": "hda", "uuid": "6852fcfe-8419-4730-b8fa-4993250b5f75"}, "primers_bed": {"id": "26b128c199b1cf27", "src": "hda", "uuid": "09d1c9df-e8dc-4ff8-ab94-214a160c2947"}, "primers_tsv": {"id": "7b481a71741f4254", "src": "hda", "uuid": "1d90e1d4-8a03-40f4-813c-02d41118e0e8"}}, "outputs": {"masked": {"id": "d80b159b87338b1a", "src": "hda", "uuid": "6accdd85-4853-4f09-ba78-b3146b23cd66"}}, "output_collections": {}, "tool_stdout": "Found 67 primers in BED file\nPrimer pair for 400_1_out_R not found in BED file.\nPrimer pair for 400_34_out_L* not found in BED file.\nPrimer pair for 400_35_out_L not found in BED file.\n400_18_out_L**\t400_23_out_R\t400_32_out_L\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "Found 67 primers in BED file\nPrimer pair for 400_1_out_R not found in BED file.\nPrimer pair for 400_34_out_L* not found in BED file.\nPrimer pair for 400_35_out_L not found in BED file.\n400_18_out_L**\t400_23_out_R\t400_32_out_L\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-26 14:41:38", "plugin": "core", "name": "end_epoch", "raw_value": "1698331298.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:41:38", "plugin": "core", "name": "start_epoch", "raw_value": "1698331298.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-0", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 0, "time_seconds": 154.7591152191162, "inputs": {"reference_genome|genome": {"src": "hda", "id": "e17916d3aaba0191"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "1", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "6eff9dee9707d390", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:44:23.522032", "create_time": "2023-10-26T14:41:59.473679", "galaxy_version": "21.09", "command_version": "jbrowse.py 0.8.0", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "c71426eac153eb4f", "external_id": "gxy-6bn76", "command_line": "mkdir -p /galaxy/server/database/jobs_directory/000/169/working/dataset_3b0c2924-0b01-4be5-a85d-0c545352a502_files && cp /galaxy/server/database/jobs_directory/000/169/configs/tmp4dmptaih /galaxy/server/database/jobs_directory/000/169/working/dataset_3b0c2924-0b01-4be5-a85d-0c545352a502_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/jobs_directory/000/169/working/dataset_3b0c2924-0b01-4be5-a85d-0c545352a502_files /galaxy/server/database/jobs_directory/000/169/configs/tmp4dmptaih && cp /galaxy/server/database/jobs_directory/000/169/configs/tmpqasoq1sd /galaxy/server/database/objects/3/b/0/dataset_3b0c2924-0b01-4be5-a85d-0c545352a502.dat; cp /galaxy/server/database/jobs_directory/000/169/configs/tmp4dmptaih /galaxy/server/database/objects/3/b/0/dataset_3b0c2924-0b01-4be5-a85d-0c545352a502.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": \"false\", \"shareLink\": \"true\", \"show_menu\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_tracklist\": \"true\", \"trackPadding\": \"20\"}", "track_groups": "[]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"1\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 277, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"genome": {"id": "e17916d3aaba0191", "src": "hda", "uuid": "47f3bd74-bac0-4091-b11d-f382e8e3b25e"}}, "outputs": {"output": {"id": "54b9e7ec611102f7", "src": "hda", "uuid": "3b0c2924-0b01-4be5-a85d-0c545352a502"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stderr": "\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-26 14:44:07", "plugin": "core", "name": "end_epoch", "raw_value": "1698331447.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:44:06", "plugin": "core", "name": "start_epoch", "raw_value": "1698331446.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-1", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 1, "time_seconds": 129.81535696983337, "inputs": {"reference_genome|genome": {"src": "hda", "id": "14e569cd8f46f142"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "25e5b19bc7c5364b", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:46:33.554171", "create_time": "2023-10-26T14:44:34.877843", "galaxy_version": "21.09", "command_version": "jbrowse.py 0.8.0", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "c71426eac153eb4f", "external_id": "gxy-zqclg", "command_line": "mkdir -p /galaxy/server/database/jobs_directory/000/171/working/dataset_7eeea2f3-a7d4-47f1-87bf-b92ab4b3c76c_files && cp /galaxy/server/database/jobs_directory/000/171/configs/tmpk65l8ohg /galaxy/server/database/jobs_directory/000/171/working/dataset_7eeea2f3-a7d4-47f1-87bf-b92ab4b3c76c_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/jobs_directory/000/171/working/dataset_7eeea2f3-a7d4-47f1-87bf-b92ab4b3c76c_files /galaxy/server/database/jobs_directory/000/171/configs/tmpk65l8ohg && cp /galaxy/server/database/jobs_directory/000/171/configs/tmpvq4x2swe /galaxy/server/database/objects/7/e/e/dataset_7eeea2f3-a7d4-47f1-87bf-b92ab4b3c76c.dat; cp /galaxy/server/database/jobs_directory/000/171/configs/tmpk65l8ohg /galaxy/server/database/objects/7/e/e/dataset_7eeea2f3-a7d4-47f1-87bf-b92ab4b3c76c.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": \"false\", \"shareLink\": \"true\", \"show_menu\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_tracklist\": \"true\", \"trackPadding\": \"20\"}", "track_groups": "[]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 279, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"genome": {"id": "14e569cd8f46f142", "src": "hda", "uuid": "38dcf7cb-5cc4-416e-8ae7-0ef491e9b0c3"}}, "outputs": {"output": {"id": "745c6089c43d4c6d", "src": "hda", "uuid": "7eeea2f3-a7d4-47f1-87bf-b92ab4b3c76c"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stderr": "\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-26 14:46:22", "plugin": "core", "name": "end_epoch", "raw_value": "1698331582.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:46:22", "plugin": "core", "name": "start_epoch", "raw_value": "1698331582.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-2", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 2, "time_seconds": 139.0890760421753, "inputs": {"reference_genome|genome": {"src": "hda", "id": "40e054ca3eb4754f"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "Default", "track_groups_0|data_tracks_0|data_format|annotation": [{"src": "hda", "id": "5e71a643b37764c1"}, {"src": "hda", "id": "0e0a0dfa7ef6cfb3"}], "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "13f2e337e1775869", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:48:52.791343", "create_time": "2023-10-26T14:46:51.405754", "galaxy_version": "21.09", "command_version": "jbrowse.py 0.8.0", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "c71426eac153eb4f", "external_id": "gxy-rv995", "command_line": "mkdir -p /galaxy/server/database/jobs_directory/000/175/working/dataset_da52263d-9aba-4450-ab2c-693db3f64a50_files && cp /galaxy/server/database/jobs_directory/000/175/configs/tmpan3weyrf /galaxy/server/database/jobs_directory/000/175/working/dataset_da52263d-9aba-4450-ab2c-693db3f64a50_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/jobs_directory/000/175/working/dataset_da52263d-9aba-4450-ab2c-693db3f64a50_files /galaxy/server/database/jobs_directory/000/175/configs/tmpan3weyrf && cp /galaxy/server/database/jobs_directory/000/175/configs/tmpta005x3w /galaxy/server/database/objects/d/a/5/dataset_da52263d-9aba-4450-ab2c-693db3f64a50.dat; cp /galaxy/server/database/jobs_directory/000/175/configs/tmpan3weyrf /galaxy/server/database/objects/d/a/5/dataset_da52263d-9aba-4450-ab2c-693db3f64a50.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": \"false\", \"shareLink\": \"true\", \"show_menu\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_tracklist\": \"true\", \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 282, \"src\": \"hda\"}, {\"id\": 283, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": \"false\", \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": \"false\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 281, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"genome": {"id": "40e054ca3eb4754f", "src": "hda", "uuid": "c7e1d5b7-42d9-41fa-bf50-5d1366755718"}, "track_groups_0|data_tracks_0|annotation": {"id": "5e71a643b37764c1", "src": "hda", "uuid": "b204cbcb-2eff-4cf0-a0d5-95cc4063006e"}, "track_groups_0|data_tracks_0|annotation1": {"id": "5e71a643b37764c1", "src": "hda", "uuid": "b204cbcb-2eff-4cf0-a0d5-95cc4063006e"}, "track_groups_0|data_tracks_0|annotation2": {"id": "0e0a0dfa7ef6cfb3", "src": "hda", "uuid": "918faf2b-1a5b-4064-a459-53642e003112"}}, "outputs": {"output": {"id": "5efc04ff24f67267", "src": "hda", "uuid": "da52263d-9aba-4450-ab2c-693db3f64a50"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "INFO:jbrowse:Processing Default / test-3.bed\nINFO:jbrowse:Processing Default / test-6.bed\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stderr": "\nINFO:jbrowse:Processing Default / test-3.bed\nINFO:jbrowse:Processing Default / test-6.bed\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-26 14:48:41", "plugin": "core", "name": "end_epoch", "raw_value": "1698331721.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:48:40", "plugin": "core", "name": "start_epoch", "raw_value": "1698331720.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-3", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 3, "time_seconds": 168.2414951324463, "inputs": {"reference_genome|genome": {"src": "hda", "id": "b1305dd09d7c0e7c"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "Auto Coloured", "track_groups_0|data_tracks_0|data_format|annotation": [{"src": "hda", "id": "5e32345f6f20ffa2"}, {"src": "hda", "id": "4eb38e519a69bd22"}, {"src": "hda", "id": "510a16069e4269ff"}, {"src": "hda", "id": "651149bdc2b7d414"}], "track_groups_0|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_1|category": "Ignore Scale", "track_groups_1|data_tracks_0|data_format|annotation": {"src": "hda", "id": "f39f6afd79e0edc1"}, "track_groups_1|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_1|data_tracks_0|data_format|jbcolor_scale|color_score|color|style_color": "#ff00ff", "track_groups_1|data_tracks_0|data_format|jbcolor_scale|color_score|color|color_select": "manual", "track_groups_1|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_1|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_2|category": "Scaled Colour", "track_groups_2|data_tracks_0|data_format|annotation": {"src": "hda", "id": "f39f6afd79e0edc1"}, "track_groups_2|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|score_scaling": "linear", "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|score_scales|scale_select": "automatic", "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|color_scheme|color|color_select": "automatic", "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|color_scheme|score_scheme": "opacity", "track_groups_2|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "score", "track_groups_2|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_2|data_tracks_1|data_format|annotation": {"src": "hda", "id": "f39f6afd79e0edc1"}, "track_groups_2|data_tracks_1|data_format|match_part|match_part_select": false, "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|score_scaling": "linear", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|score_scales|scale_select": "automatic", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_scheme|color|style_color": "#0000ff", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_scheme|color|color_select": "manual", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_scheme|score_scheme": "opacity", "track_groups_2|data_tracks_1|data_format|jbcolor_scale|color_score|color_score_select": "score", "track_groups_2|data_tracks_1|data_format|data_format_select": "gene_calls", "track_groups_2|data_tracks_2|data_format|annotation": {"src": "hda", "id": "f39f6afd79e0edc1"}, "track_groups_2|data_tracks_2|data_format|match_part|match_part_select": false, "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scaling": "linear", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scales|minimum": "0", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scales|maximum": "1000", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|score_scales|scale_select": "manual", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|color_scheme|color|color_select": "automatic", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|color_scheme|score_scheme": "opacity", "track_groups_2|data_tracks_2|data_format|jbcolor_scale|color_score|color_score_select": "score", "track_groups_2|data_tracks_2|data_format|data_format_select": "gene_calls", "track_groups_2|data_tracks_3|data_format|annotation": {"src": "hda", "id": "f39f6afd79e0edc1"}, "track_groups_2|data_tracks_3|data_format|match_part|match_part_select": false, "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scaling": "linear", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scales|minimum": "0", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scales|maximum": "1000", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|score_scales|scale_select": "manual", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_scheme|color|style_color": "#ff0000", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_scheme|color|color_select": "manual", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_scheme|score_scheme": "opacity", "track_groups_2|data_tracks_3|data_format|jbcolor_scale|color_score|color_score_select": "score", "track_groups_2|data_tracks_3|data_format|data_format_select": "gene_calls", "track_groups_3|category": "Realistic", "track_groups_3|data_tracks_0|data_format|annotation": {"src": "hda", "id": "5e0a41cbacfd46a7"}, "track_groups_3|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_3|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_3|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_3|data_tracks_1|data_format|annotation": {"src": "hda", "id": "ce43ff90e9e479c1"}, "track_groups_3|data_tracks_1|data_format|match_part|name": "cDNA_match", "track_groups_3|data_tracks_1|data_format|match_part|match_part_select": true, "track_groups_3|data_tracks_1|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_3|data_tracks_1|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "1031c14ed32190e7", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:51:40.881992", "create_time": "2023-10-26T14:49:37.573642", "galaxy_version": "21.09", "command_version": "jbrowse.py 0.8.0", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "c71426eac153eb4f", "external_id": "gxy-2sh88", "command_line": "mkdir -p /galaxy/server/database/jobs_directory/000/184/working/dataset_6a92a499-0d3f-4da2-8603-69d66f49e860_files && cp /galaxy/server/database/jobs_directory/000/184/configs/tmprmmsgahb /galaxy/server/database/jobs_directory/000/184/working/dataset_6a92a499-0d3f-4da2-8603-69d66f49e860_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/jobs_directory/000/184/working/dataset_6a92a499-0d3f-4da2-8603-69d66f49e860_files /galaxy/server/database/jobs_directory/000/184/configs/tmprmmsgahb && cp /galaxy/server/database/jobs_directory/000/184/configs/tmpb8aqza3_ /galaxy/server/database/objects/6/a/9/dataset_6a92a499-0d3f-4da2-8603-69d66f49e860.dat; cp /galaxy/server/database/jobs_directory/000/184/configs/tmprmmsgahb /galaxy/server/database/objects/6/a/9/dataset_6a92a499-0d3f-4da2-8603-69d66f49e860.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": \"false\", \"shareLink\": \"true\", \"show_menu\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_tracklist\": \"true\", \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"Auto Coloured\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 286, \"src\": \"hda\"}, {\"id\": 287, \"src\": \"hda\"}, {\"id\": 288, \"src\": \"hda\"}, {\"id\": 289, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": \"false\", \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": \"false\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 1, \"category\": \"Ignore Scale\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 290, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": \"false\", \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 1, \"color_select\": \"manual\", \"style_color\": \"#ff00ff\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": \"false\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 2, \"category\": \"Scaled Colour\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 290, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": \"false\", \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 1, \"color_scheme\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"score_scheme\": \"opacity\"}, \"color_score_select\": \"score\", \"score_scales\": {\"__current_case__\": 0, \"scale_select\": \"automatic\"}, \"score_scaling\": \"linear\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": \"false\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 290, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": \"false\", \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 1, \"color_scheme\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 1, \"color_select\": \"manual\", \"style_color\": \"#0000ff\"}, \"score_scheme\": \"opacity\"}, \"color_score_select\": \"score\", \"score_scales\": {\"__current_case__\": 0, \"scale_select\": \"automatic\"}, \"score_scaling\": \"linear\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": \"false\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 2, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 290, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": \"false\", \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 1, \"color_scheme\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"score_scheme\": \"opacity\"}, \"color_score_select\": \"score\", \"score_scales\": {\"__current_case__\": 1, \"maximum\": \"1000\", \"minimum\": \"0\", \"scale_select\": \"manual\"}, \"score_scaling\": \"linear\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": \"false\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 3, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 290, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": \"false\", \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 1, \"color_scheme\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 1, \"color_select\": \"manual\", \"style_color\": \"#ff0000\"}, \"score_scheme\": \"opacity\"}, \"color_score_select\": \"score\", \"score_scales\": {\"__current_case__\": 1, \"maximum\": \"1000\", \"minimum\": \"0\", \"scale_select\": \"manual\"}, \"score_scaling\": \"linear\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": \"false\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}, {\"__index__\": 3, \"category\": \"Realistic\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 291, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": \"false\", \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": \"false\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 292, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": \"false\", \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 0, \"match_part_select\": \"true\", \"name\": \"cDNA_match\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 285, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"genome": {"id": "b1305dd09d7c0e7c", "src": "hda", "uuid": "91b78482-6277-4af7-b402-8437a345788d"}, "track_groups_0|data_tracks_0|annotation": {"id": "5e32345f6f20ffa2", "src": "hda", "uuid": "7c88bc47-39c3-4ce7-966b-3f1f65d310c0"}, "track_groups_0|data_tracks_0|annotation1": {"id": "5e32345f6f20ffa2", "src": "hda", "uuid": "7c88bc47-39c3-4ce7-966b-3f1f65d310c0"}, "track_groups_0|data_tracks_0|annotation2": {"id": "4eb38e519a69bd22", "src": "hda", "uuid": "22192d28-76e7-4c9a-8d70-3f419eb34e54"}, "track_groups_0|data_tracks_0|annotation3": {"id": "510a16069e4269ff", "src": "hda", "uuid": "98984803-08dc-4ee0-ac9e-beace80fc380"}, "track_groups_0|data_tracks_0|annotation4": {"id": "651149bdc2b7d414", "src": "hda", "uuid": "23306b6b-1d26-4099-a575-ee293b5d1a3e"}, "track_groups_1|data_tracks_0|annotation": {"id": "f39f6afd79e0edc1", "src": "hda", "uuid": "5a275a36-4318-4528-a8d2-4cba7e765643"}, "track_groups_2|data_tracks_0|annotation": {"id": "f39f6afd79e0edc1", "src": "hda", "uuid": "5a275a36-4318-4528-a8d2-4cba7e765643"}, "track_groups_2|data_tracks_1|annotation": {"id": "f39f6afd79e0edc1", "src": "hda", "uuid": "5a275a36-4318-4528-a8d2-4cba7e765643"}, "track_groups_2|data_tracks_2|annotation": {"id": "f39f6afd79e0edc1", "src": "hda", "uuid": "5a275a36-4318-4528-a8d2-4cba7e765643"}, "track_groups_2|data_tracks_3|annotation": {"id": "f39f6afd79e0edc1", "src": "hda", "uuid": "5a275a36-4318-4528-a8d2-4cba7e765643"}, "track_groups_3|data_tracks_0|annotation": {"id": "5e0a41cbacfd46a7", "src": "hda", "uuid": "908639fe-b3bf-46c9-81db-d425fb223e00"}, "track_groups_3|data_tracks_1|annotation": {"id": "ce43ff90e9e479c1", "src": "hda", "uuid": "47438d85-5054-4631-a7e1-ef951f9324dd"}}, "outputs": {"output": {"id": "fb6b2e1088fe78dd", "src": "hda", "uuid": "6a92a499-0d3f-4da2-8603-69d66f49e860"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "INFO:jbrowse:Processing Auto Coloured / A.gff\nINFO:jbrowse:Processing Auto Coloured / B.gff\nINFO:jbrowse:Processing Auto Coloured / C.gff\nINFO:jbrowse:Processing Auto Coloured / D.gff\nINFO:jbrowse:Processing Ignore Scale / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Realistic / interpro.gff\nINFO:jbrowse:Processing Realistic / 2.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stderr": "\nINFO:jbrowse:Processing Auto Coloured / A.gff\nINFO:jbrowse:Processing Auto Coloured / B.gff\nINFO:jbrowse:Processing Auto Coloured / C.gff\nINFO:jbrowse:Processing Auto Coloured / D.gff\nINFO:jbrowse:Processing Ignore Scale / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Scaled Colour / 1.gff\nINFO:jbrowse:Processing Realistic / interpro.gff\nINFO:jbrowse:Processing Realistic / 2.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2023-10-26 14:51:30", "plugin": "core", "name": "end_epoch", "raw_value": "1698331890.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:51:27", "plugin": "core", "name": "start_epoch", "raw_value": "1698331887.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-4", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 4, "time_seconds": 136.00378680229187, "inputs": {"reference_genome|genome": {"src": "hda", "id": "417ed522e7d772f3"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "With menu or index", "track_groups_0|data_tracks_0|data_format|annotation": {"src": "hda", "id": "2da77251dc87a6ef"}, "track_groups_0|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_action": "iframeDialog", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_label": "Some menu item", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_title": "Frame title", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_url": "https://example.com/#!/?id={name}&q={type}&z=\"{end}\"", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_0|menu_icon": "dijitIconNewTask", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_action": "newWindow", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_label": "Another menu item", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_title": "Frame title 2", "track_groups_0|data_tracks_0|data_format|jbmenu|track_menu_1|menu_url": "https://example.com/#!/?id={name}&q={type}&z=\"{end}\"", "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "track_groups_0|data_tracks_1|data_format|annotation": {"src": "hda", "id": "2da77251dc87a6ef"}, "track_groups_0|data_tracks_1|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_1|data_format|index": true, "track_groups_0|data_tracks_1|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_1|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "bcdc112a0df266ca", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:53:56.912070", "create_time": "2023-10-26T14:51:53.445166", "galaxy_version": "21.09", "command_version": "jbrowse.py 0.8.0", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "c71426eac153eb4f", "external_id": "gxy-5h5sz", "command_line": "mkdir -p /galaxy/server/database/jobs_directory/000/187/working/dataset_77d610e3-b43e-414f-8c51-f578ae6cb842_files && cp /galaxy/server/database/jobs_directory/000/187/configs/tmpap3de9v_ /galaxy/server/database/jobs_directory/000/187/working/dataset_77d610e3-b43e-414f-8c51-f578ae6cb842_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/jobs_directory/000/187/working/dataset_77d610e3-b43e-414f-8c51-f578ae6cb842_files /galaxy/server/database/jobs_directory/000/187/configs/tmpap3de9v_ && cp /galaxy/server/database/jobs_directory/000/187/configs/tmpj4rly172 /galaxy/server/database/objects/7/7/d/dataset_77d610e3-b43e-414f-8c51-f578ae6cb842.dat; cp /galaxy/server/database/jobs_directory/000/187/configs/tmpap3de9v_ /galaxy/server/database/objects/7/7/d/dataset_77d610e3-b43e-414f-8c51-f578ae6cb842.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": \"false\", \"shareLink\": \"true\", \"show_menu\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_tracklist\": \"true\", \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"With menu or index\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 295, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": \"false\", \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": [{\"__index__\": 0, \"menu_action\": \"iframeDialog\", \"menu_icon\": \"dijitIconNewTask\", \"menu_label\": \"Some menu item\", \"menu_title\": \"Frame title\", \"menu_url\": \"https://example.com/#!/?id={name}&q={type}&z=\\\"{end}\\\"\"}, {\"__index__\": 1, \"menu_action\": \"newWindow\", \"menu_icon\": \"dijitIconBookmark\", \"menu_label\": \"Another menu item\", \"menu_title\": \"Frame title 2\", \"menu_url\": \"https://example.com/#!/?id={name}&q={type}&z=\\\"{end}\\\"\"}]}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": \"false\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 295, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": \"true\", \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": \"false\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 294, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"genome": {"id": "417ed522e7d772f3", "src": "hda", "uuid": "72a04089-8890-435d-975a-a9adfa1f1951"}, "track_groups_0|data_tracks_0|annotation": {"id": "2da77251dc87a6ef", "src": "hda", "uuid": "955b29c8-bb6e-4865-a54b-9bb882e5182b"}, "track_groups_0|data_tracks_1|annotation": {"id": "2da77251dc87a6ef", "src": "hda", "uuid": "955b29c8-bb6e-4865-a54b-9bb882e5182b"}}, "outputs": {"output": {"id": "1860729c5d5ad59a", "src": "hda", "uuid": "77d610e3-b43e-414f-8c51-f578ae6cb842"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "INFO:jbrowse:Processing With menu or index / 1.gff\nINFO:jbrowse:Processing With menu or index / 1.gff\n", "stderr": "\nINFO:jbrowse:Processing With menu or index / 1.gff\nINFO:jbrowse:Processing With menu or index / 1.gff\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2023-10-26 14:53:45", "plugin": "core", "name": "end_epoch", "raw_value": "1698332025.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:53:43", "plugin": "core", "name": "start_epoch", "raw_value": "1698332023.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-5", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 5, "time_seconds": 137.17891454696655, "inputs": {"reference_genome|genome": {"src": "hda", "id": "0575503516b53082"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "With canvas config", "track_groups_0|data_tracks_0|data_format|annotation": {"src": "hda", "id": "b48f90cc3e7d16dd"}, "track_groups_0|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_0|data_format|track_config|canvas_options|transcriptType": "transcript", "track_groups_0|data_tracks_0|data_format|track_config|canvas_options|subParts": "exon", "track_groups_0|data_tracks_0|data_format|track_config|canvas_options|impliedUTRs": true, "track_groups_0|data_tracks_0|data_format|track_config|track_class": "JBrowse/View/Track/CanvasFeatures", "track_groups_0|data_tracks_0|data_format|jbcolor_scale|color_score|color_score_select": "none", "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "df566c89ae7a76db", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:56:14.289802", "create_time": "2023-10-26T14:54:09.847509", "galaxy_version": "21.09", "command_version": "jbrowse.py 0.8.0", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "c71426eac153eb4f", "external_id": "gxy-94p2f", "command_line": "mkdir -p /galaxy/server/database/jobs_directory/000/190/working/dataset_e609020a-3244-49e0-9bbb-4d5efa5ca268_files && cp /galaxy/server/database/jobs_directory/000/190/configs/tmpzfl5s534 /galaxy/server/database/jobs_directory/000/190/working/dataset_e609020a-3244-49e0-9bbb-4d5efa5ca268_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/jobs_directory/000/190/working/dataset_e609020a-3244-49e0-9bbb-4d5efa5ca268_files /galaxy/server/database/jobs_directory/000/190/configs/tmpzfl5s534 && cp /galaxy/server/database/jobs_directory/000/190/configs/tmpx1k1dmw1 /galaxy/server/database/objects/e/6/0/dataset_e609020a-3244-49e0-9bbb-4d5efa5ca268.dat; cp /galaxy/server/database/jobs_directory/000/190/configs/tmpzfl5s534 /galaxy/server/database/objects/e/6/0/dataset_e609020a-3244-49e0-9bbb-4d5efa5ca268.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": \"false\", \"shareLink\": \"true\", \"show_menu\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_tracklist\": \"true\", \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"With canvas config\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 298, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": \"false\", \"jb_custom_config\": {\"option\": []}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": \"false\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 0, \"canvas_options\": {\"impliedUTRs\": \"true\", \"subParts\": \"exon\", \"transcriptType\": \"transcript\"}, \"track_class\": \"JBrowse/View/Track/CanvasFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 297, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"genome": {"id": "0575503516b53082", "src": "hda", "uuid": "973ff4d7-0ab1-40d6-b144-0c0c9de6fc72"}, "track_groups_0|data_tracks_0|annotation": {"id": "b48f90cc3e7d16dd", "src": "hda", "uuid": "dda912d7-75ef-44e3-a7e3-3f7dfa1d90c3"}}, "outputs": {"output": {"id": "2bb2dfdc4a4f596f", "src": "hda", "uuid": "e609020a-3244-49e0-9bbb-4d5efa5ca268"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "INFO:jbrowse:Processing With canvas config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stderr": "\nINFO:jbrowse:Processing With canvas config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-26 14:56:04", "plugin": "core", "name": "end_epoch", "raw_value": "1698332164.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:56:03", "plugin": "core", "name": "start_epoch", "raw_value": "1698332163.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-6", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 6, "time_seconds": 135.57516813278198, "inputs": {"reference_genome|genome": {"src": "hda", "id": "0c7336382acca128"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "With custom track config", "track_groups_0|data_tracks_0|data_format|annotation": {"src": "hda", "id": "3225ef60c92b589e"}, "track_groups_0|data_tracks_0|data_format|match_part|match_part_select": false, "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_0|opt_key": "displayMode", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_0|opt_value|val": "collapsed", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_0|opt_value|val_type": "text", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_1|opt_key": "histograms.height", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_1|opt_value|val": "150", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_1|opt_value|val_type": "integer", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_2|opt_key": "maxFeatureScreenDensity", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_2|opt_value|val": "0.1", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_2|opt_value|val_type": "float", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_3|opt_key": "style.strandArrow", "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_3|opt_value|val": false, "track_groups_0|data_tracks_0|data_format|jb_custom_config|option_3|opt_value|val_type": "boolean", "track_groups_0|data_tracks_0|data_format|data_format_select": "gene_calls", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "178047eb94a6079a", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:58:29.793519", "create_time": "2023-10-26T14:56:27.018298", "galaxy_version": "21.09", "command_version": "jbrowse.py 0.8.0", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "c71426eac153eb4f", "external_id": "gxy-gdgfv", "command_line": "mkdir -p /galaxy/server/database/jobs_directory/000/193/working/dataset_d80b1ba4-a477-498d-a3cf-f6e6647e596a_files && cp /galaxy/server/database/jobs_directory/000/193/configs/tmp3ll4jl6s /galaxy/server/database/jobs_directory/000/193/working/dataset_d80b1ba4-a477-498d-a3cf-f6e6647e596a_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/jobs_directory/000/193/working/dataset_d80b1ba4-a477-498d-a3cf-f6e6647e596a_files /galaxy/server/database/jobs_directory/000/193/configs/tmp3ll4jl6s && cp /galaxy/server/database/jobs_directory/000/193/configs/tmpk43ynb9p /galaxy/server/database/objects/d/8/0/dataset_d80b1ba4-a477-498d-a3cf-f6e6647e596a.dat; cp /galaxy/server/database/jobs_directory/000/193/configs/tmp3ll4jl6s /galaxy/server/database/objects/d/8/0/dataset_d80b1ba4-a477-498d-a3cf-f6e6647e596a.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": \"false\", \"shareLink\": \"true\", \"show_menu\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_tracklist\": \"true\", \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"With custom track config\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 2, \"annotation\": {\"values\": [{\"id\": 301, \"src\": \"hda\"}]}, \"data_format_select\": \"gene_calls\", \"index\": \"false\", \"jb_custom_config\": {\"option\": [{\"__index__\": 0, \"opt_key\": \"displayMode\", \"opt_value\": {\"__current_case__\": 0, \"val\": \"collapsed\", \"val_type\": \"text\"}}, {\"__index__\": 1, \"opt_key\": \"histograms.height\", \"opt_value\": {\"__current_case__\": 1, \"val\": \"150\", \"val_type\": \"integer\"}}, {\"__index__\": 2, \"opt_key\": \"maxFeatureScreenDensity\", \"opt_value\": {\"__current_case__\": 2, \"val\": \"0.1\", \"val_type\": \"float\"}}, {\"__index__\": 3, \"opt_key\": \"style.strandArrow\", \"opt_value\": {\"__current_case__\": 3, \"val\": \"false\", \"val_type\": \"boolean\"}}]}, \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"style_label\": \"product,name,id\"}, \"match_part\": {\"__current_case__\": 1, \"match_part_select\": \"false\"}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_config\": {\"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}, \"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\"}, \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 300, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"genome": {"id": "0c7336382acca128", "src": "hda", "uuid": "5203b2c5-1109-4b4d-81da-e6ccbb098254"}, "track_groups_0|data_tracks_0|annotation": {"id": "3225ef60c92b589e", "src": "hda", "uuid": "476aaa8a-1820-4a82-9a6b-35cc0cf16275"}}, "outputs": {"output": {"id": "56ef7d2486c35295", "src": "hda", "uuid": "d80b1ba4-a477-498d-a3cf-f6e6647e596a"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "INFO:jbrowse:Processing With custom track config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stderr": "\nINFO:jbrowse:Processing With custom track config / 1.gff\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-26 14:58:19", "plugin": "core", "name": "end_epoch", "raw_value": "1698332299.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:58:18", "plugin": "core", "name": "start_epoch", "raw_value": "1698332298.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-7", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 7, "time_seconds": 136.36756348609924, "inputs": {"reference_genome|genome": {"src": "hda", "id": "497487a1abc55104"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "Auto Coloured", "track_groups_0|data_tracks_0|data_format|annotation": {"src": "hda", "id": "c2fdd6ad5a833d12"}, "track_groups_0|data_tracks_0|data_format|data_format_select": "pileup", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "a8669dab5b0064df", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T15:00:46.294867", "create_time": "2023-10-26T14:58:42.454543", "galaxy_version": "21.09", "command_version": "jbrowse.py 0.8.0", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "c71426eac153eb4f", "external_id": "gxy-vmb79", "command_line": "mkdir -p /galaxy/server/database/jobs_directory/000/196/working/dataset_8a20e848-8df6-437a-9522-7315006e1ca7_files && cp /galaxy/server/database/jobs_directory/000/196/configs/tmpnc2favni /galaxy/server/database/jobs_directory/000/196/working/dataset_8a20e848-8df6-437a-9522-7315006e1ca7_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/jobs_directory/000/196/working/dataset_8a20e848-8df6-437a-9522-7315006e1ca7_files /galaxy/server/database/jobs_directory/000/196/configs/tmpnc2favni && cp /galaxy/server/database/jobs_directory/000/196/configs/tmpe22569kc /galaxy/server/database/objects/8/a/2/dataset_8a20e848-8df6-437a-9522-7315006e1ca7.dat; cp /galaxy/server/database/jobs_directory/000/196/configs/tmpnc2favni /galaxy/server/database/objects/8/a/2/dataset_8a20e848-8df6-437a-9522-7315006e1ca7.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": \"false\", \"shareLink\": \"true\", \"show_menu\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_tracklist\": \"true\", \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"Auto Coloured\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 3, \"annotation\": {\"values\": [{\"id\": 304, \"src\": \"hda\"}]}, \"auto_snp\": \"false\", \"chunkSizeLimit\": \"5000000\", \"data_format_select\": \"pileup\", \"jb_custom_config\": {\"option\": []}, \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_visibility\": \"default_off\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 303, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"genome": {"id": "497487a1abc55104", "src": "hda", "uuid": "c6dbe43a-87ed-4d8c-83f4-b4636502bf14"}, "track_groups_0|data_tracks_0|annotation": {"id": "c2fdd6ad5a833d12", "src": "hda", "uuid": "d551c5e1-7fbf-4aae-973c-ba99ec436f28"}}, "outputs": {"output": {"id": "43f1b9c7f768ab42", "src": "hda", "uuid": "8a20e848-8df6-437a-9522-7315006e1ca7"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "INFO:jbrowse:Processing Auto Coloured / merlin-sample.bam\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stderr": "\nINFO:jbrowse:Processing Auto Coloured / merlin-sample.bam\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-26 15:00:36", "plugin": "core", "name": "end_epoch", "raw_value": "1698332436.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 15:00:35", "plugin": "core", "name": "start_epoch", "raw_value": "1698332435.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "jbrowse/1.16.11+galaxy1-8", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 8, "time_seconds": 266.75051856040955, "inputs": {"reference_genome|genome_type_select": "indexed", "standalone": "data", "gencode": "1", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "5e3ce93f9640e07c", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T15:05:13.450331", "create_time": "2023-10-26T15:00:47.063298", "galaxy_version": "21.09", "command_version": "jbrowse.py 0.8.0", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "c71426eac153eb4f", "external_id": "gxy-998bh", "command_line": "mkdir -p /galaxy/server/database/jobs_directory/000/197/working/dataset_e58a4920-7691-4922-94e7-dfe8e95f7e9b_files && cp /galaxy/server/database/jobs_directory/000/197/configs/tmpx10i6ckg /galaxy/server/database/jobs_directory/000/197/working/dataset_e58a4920-7691-4922-94e7-dfe8e95f7e9b_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/jobs_directory/000/197/working/dataset_e58a4920-7691-4922-94e7-dfe8e95f7e9b_files /galaxy/server/database/jobs_directory/000/197/configs/tmpx10i6ckg && cp /galaxy/server/database/jobs_directory/000/197/configs/tmpgk0ovpxn /galaxy/server/database/objects/e/5/8/dataset_e58a4920-7691-4922-94e7-dfe8e95f7e9b.dat; cp /galaxy/server/database/jobs_directory/000/197/configs/tmpx10i6ckg /galaxy/server/database/objects/e/5/8/dataset_e58a4920-7691-4922-94e7-dfe8e95f7e9b.dat", "traceback": null, "params": {"__input_ext": "\"data\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": \"false\", \"shareLink\": \"true\", \"show_menu\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_tracklist\": \"true\", \"trackPadding\": \"20\"}", "track_groups": "[]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"1\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 0, \"genome_type_select\": \"indexed\", \"genomes\": \"apiMel4\"}"}, "inputs": {}, "outputs": {"output": {"id": "420365c1f21d9f39", "src": "hda", "uuid": "e58a4920-7691-4922-94e7-dfe8e95f7e9b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "WARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stderr": "\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "65.0000000"}, {"title": "Job End Time", "value": "2023-10-26 15:03:44", "plugin": "core", "name": "end_epoch", "raw_value": "1698332624.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 15:02:39", "plugin": "core", "name": "start_epoch", "raw_value": "1698332559.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: different than expected\nExpected text 'merlin.fa' in output ('\n\n \n 1\n \n \n \n s\n \n \n \n 20\n\n true\n \n true\n true\n true\n true\n false\n \n http://localhost:8080\n \n \n \n \n\n')"], "status": "failure"}}, {"id": "jbrowse/1.16.11+galaxy1-9", "has_data": true, "data": {"tool_id": "jbrowse", "tool_version": "1.16.11+galaxy1", "test_index": 9, "time_seconds": 129.63591408729553, "inputs": {"reference_genome|genome": {"src": "hda", "id": "99eda6e8e5d5ef71"}, "reference_genome|genome_type_select": "history", "standalone": "data", "gencode": "11", "track_groups_0|category": "External endpoints", "track_groups_0|data_tracks_0|data_format|url": "http://example.org.external/rest_api/", "track_groups_0|data_tracks_0|data_format|label": "Rest api", "track_groups_0|data_tracks_0|data_format|data_format_select": "rest", "track_groups_0|data_tracks_1|data_format|url": "http://example.org.external/sparql/", "track_groups_0|data_tracks_1|data_format|label": "Sparql endpoint", "track_groups_0|data_tracks_1|data_format|query": " DEFINE sql:select-option 'order' prefix rdf: select ?start, ?end, IF( ?faldo_type = faldo:ForwardStrandPosition, 1, IF( ?faldo_type = faldo:ReverseStrandPosition, -1, 0 ) ) as ?strand, str(?obj_type_name) as ?type, str(?label) as ?name, str(?obj_name) as ?description, ?obj as ?uniqueID, ?parent as ?parentUniqueID where { values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } }", "track_groups_0|data_tracks_1|data_format|data_format_select": "sparql", "uglyTestingHack": "enabled"}, "job": {"model_class": "Job", "id": "936bbdad97015d85", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T15:07:23.009177", "create_time": "2023-10-26T15:05:23.335149", "galaxy_version": "21.09", "command_version": "jbrowse.py 0.8.0", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "history_id": "c71426eac153eb4f", "external_id": "gxy-7g422", "command_line": "mkdir -p /galaxy/server/database/jobs_directory/000/199/working/dataset_95040f90-72e2-47f3-9738-b6da6861bde1_files && cp /galaxy/server/database/jobs_directory/000/199/configs/tmpfeyq4i8q /galaxy/server/database/jobs_directory/000/199/working/dataset_95040f90-72e2-47f3-9738-b6da6861bde1_files/galaxy.xml && export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'data' --outdir /galaxy/server/database/jobs_directory/000/199/working/dataset_95040f90-72e2-47f3-9738-b6da6861bde1_files /galaxy/server/database/jobs_directory/000/199/configs/tmpfeyq4i8q && cp /galaxy/server/database/jobs_directory/000/199/configs/tmpd7uwqo8g /galaxy/server/database/objects/9/5/0/dataset_95040f90-72e2-47f3-9738-b6da6861bde1.dat; cp /galaxy/server/database/jobs_directory/000/199/configs/tmpfeyq4i8q /galaxy/server/database/objects/9/5/0/dataset_95040f90-72e2-47f3-9738-b6da6861bde1.dat", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "uglyTestingHack": "\"enabled\"", "plugins": "{\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}", "jbgen": "{\"aboutDescription\": \"\", \"defaultLocation\": \"\", \"hideGenomeOptions\": \"false\", \"shareLink\": \"true\", \"show_menu\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_tracklist\": \"true\", \"trackPadding\": \"20\"}", "track_groups": "[{\"__index__\": 0, \"category\": \"External endpoints\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"__current_case__\": 5, \"data_format_select\": \"rest\", \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"Hit_titles\", \"style_height\": \"600px\", \"style_label\": \"description\"}, \"label\": \"Rest api\", \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"track_visibility\": \"default_off\", \"url\": \"http://example.org.external/rest_api/\"}}, {\"__index__\": 1, \"data_format\": {\"__current_case__\": 6, \"data_format_select\": \"sparql\", \"jbcolor_scale\": {\"color_score\": {\"__current_case__\": 0, \"color\": {\"__current_case__\": 0, \"color_select\": \"automatic\"}, \"color_score_select\": \"none\"}}, \"jbmenu\": {\"track_menu\": []}, \"jbstyle\": {\"max_height\": \"600\", \"style_classname\": \"feature\", \"style_description\": \"Hit_titles\", \"style_height\": \"600px\", \"style_label\": \"description\"}, \"label\": \"Sparql endpoint\", \"override_apollo_drag\": \"False\", \"override_apollo_plugins\": \"False\", \"query\": \" DEFINE sql:select-option 'order' prefix rdf: select ?start, ?end, IF( ?faldo_type = faldo:ForwardStrandPosition, 1, IF( ?faldo_type = faldo:ReverseStrandPosition, -1, 0 ) ) as ?strand, str(?obj_type_name) as ?type, str(?label) as ?name, str(?obj_name) as ?description, ?obj as ?uniqueID, ?parent as ?parentUniqueID where { values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } }\", \"track_visibility\": \"default_off\", \"url\": \"http://example.org.external/sparql/\"}}]}]", "action": "{\"__current_case__\": 0, \"action_select\": \"create\"}", "gencode": "\"11\"", "standalone": "\"data\"", "reference_genome": "{\"__current_case__\": 1, \"genome\": {\"values\": [{\"id\": 307, \"src\": \"hda\"}]}, \"genome_type_select\": \"history\"}"}, "inputs": {"genome": {"id": "99eda6e8e5d5ef71", "src": "hda", "uuid": "9df43f3d-e1f0-46ce-a346-27cdcfe80b95"}}, "outputs": {"output": {"id": "03c923cd0534e4b4", "src": "hda", "uuid": "95040f90-72e2-47f3-9738-b6da6861bde1"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "INFO:jbrowse:Processing External endpoints / Rest api\nINFO:jbrowse:Processing External endpoints / Sparql endpoint\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stderr": "\nINFO:jbrowse:Processing External endpoints / Rest api\nINFO:jbrowse:Processing External endpoints / Sparql endpoint\nWARNING: No feature names found for indexing, only reference sequence names will be indexed.\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-26 15:07:13", "plugin": "core", "name": "end_epoch", "raw_value": "1698332833.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 15:07:12", "plugin": "core", "name": "start_epoch", "raw_value": "1698332832.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "lofreq_call/2.1.5+galaxy2-0", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 0, "time_seconds": 137.08009791374207, "inputs": {"reads": {"src": "hda", "id": "1dcdb09bf9895815"}, "reference_source|ref": {"src": "hda", "id": "3c6041f408fcae69"}, "reference_source|ref_selector": "history"}, "job": {"model_class": "Job", "id": "bf3bc80c8588c491", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:30:21.393383", "create_time": "2023-10-26T14:28:16.084633", "galaxy_version": "21.09", "command_version": "2.1.5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "history_id": "c71426eac153eb4f", "external_id": "gxy-cfh45", "command_line": "ln -s '/galaxy/server/database/objects/0/d/6/dataset_0d627cfa-e39e-419b-9209-3187b793e057.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/d/a/9/dataset_da9e05fd-1679-4e43-8b00-29bfa550ccbf.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/2/d/2/metadata_2d29354d-5aca-4e6a-84cc-28b91fd2113c.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 2, \"bonf\": \"dynamic\", \"filter_type\": \"set_lofreq_standard\", \"others\": \"\", \"sig\": \"0.01\"}", "call_control": "{\"__current_case__\": 0, \"set_call_options\": \"no\"}", "variant_types": "\"\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 258, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "1dcdb09bf9895815", "src": "hda", "uuid": "da9e05fd-1679-4e43-8b00-29bfa550ccbf"}, "ref": {"id": "3c6041f408fcae69", "src": "hda", "uuid": "0d627cfa-e39e-419b-9209-3187b793e057"}}, "outputs": {"variants": {"id": "ab3fb0fe2c68695c", "src": "hda", "uuid": "6823e1e2-acee-4da6-866f-0fab4cf7cafd"}}, "output_collections": {}, "tool_stdout": "INFO [2023-10-26 14:30:09,624]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2023-10-26 14:30:09,638]: Adding 3 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2023-10-26 14:30:11,503]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/150/tmp/lofreq2_call_parallel6gkxtvqx/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "INFO [2023-10-26 14:30:09,624]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2023-10-26 14:30:09,638]: Adding 3 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2023-10-26 14:30:11,503]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/150/tmp/lofreq2_call_parallel6gkxtvqx/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2023-10-26 14:30:11", "plugin": "core", "name": "end_epoch", "raw_value": "1698330611.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:30:09", "plugin": "core", "name": "start_epoch", "raw_value": "1698330609.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "lofreq_call/2.1.5+galaxy2-1", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 1, "time_seconds": 134.7064151763916, "inputs": {"reads": {"src": "hda", "id": "371dc975b8095890"}, "reference_source|ref": {"src": "hda", "id": "9ebc5a1ec1690fdb"}, "reference_source|ref_selector": "history", "call_control|set_call_options": "yes"}, "job": {"model_class": "Job", "id": "099e07fa17a7676a", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:32:36.005303", "create_time": "2023-10-26T14:30:33.048564", "galaxy_version": "21.09", "command_version": "2.1.5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "history_id": "c71426eac153eb4f", "external_id": "gxy-qrg88", "command_line": "ln -s '/galaxy/server/database/objects/b/a/8/dataset_ba8e21ab-a626-4462-adb8-94b5e38c435d.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/3/4/9/dataset_3496ee01-05ab-46fa-b8d4-5e409cd51273.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/a/d/8/metadata_ad8c77be-c619-47f6-8751-b2264e20ac2e.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 2, \"bonf\": \"dynamic\", \"filter_type\": \"set_lofreq_standard\", \"others\": \"\", \"sig\": \"0.01\"}", "call_control": "{\"__current_case__\": 1, \"align_quals\": {\"alnqual\": {\"__current_case__\": 0, \"alnqual_choice\": {\"__current_case__\": 1, \"alnquals_to_use\": \"\", \"extended_baq\": \"true\"}, \"use_alnqual\": \"\"}}, \"bc_quals\": {\"alt_bq\": {\"__current_case__\": 0, \"modify\": \"\"}, \"min_alt_bq\": \"6\", \"min_bq\": \"6\"}, \"coverage\": {\"max_depth\": \"1000000\", \"min_cov\": \"1\"}, \"joint_qual\": {\"def_alt_jq\": \"0\", \"min_alt_jq\": \"0\", \"min_jq\": \"0\"}, \"map_quals\": {\"min_mq\": \"0\", \"use_mq\": {\"__current_case__\": 0, \"max_mq\": \"255\", \"no_mq\": \"\"}}, \"pe\": {\"use_orphan\": \"false\"}, \"set_call_options\": \"yes\", \"source_qual\": {\"use_src_qual\": {\"__current_case__\": 0, \"src_qual\": \"\"}}}", "variant_types": "\"\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 261, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "371dc975b8095890", "src": "hda", "uuid": "3496ee01-05ab-46fa-b8d4-5e409cd51273"}, "ref": {"id": "9ebc5a1ec1690fdb", "src": "hda", "uuid": "ba8e21ab-a626-4462-adb8-94b5e38c435d"}}, "outputs": {"variants": {"id": "46ce66fe758e4454", "src": "hda", "uuid": "5d08a6f5-980a-4430-8ade-db25c630a8b3"}}, "output_collections": {}, "tool_stdout": "INFO [2023-10-26 14:32:24,663]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2023-10-26 14:32:24,681]: Adding 3 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2023-10-26 14:32:26,625]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/153/tmp/lofreq2_call_parallelvshbl95q/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "INFO [2023-10-26 14:32:24,663]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2023-10-26 14:32:24,681]: Adding 3 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2023-10-26 14:32:26,625]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/153/tmp/lofreq2_call_parallelvshbl95q/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2023-10-26 14:32:26", "plugin": "core", "name": "end_epoch", "raw_value": "1698330746.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:32:24", "plugin": "core", "name": "start_epoch", "raw_value": "1698330744.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "lofreq_call/2.1.5+galaxy2-2", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 2, "time_seconds": 141.1240439414978, "inputs": {"reads": {"src": "hda", "id": "2eda2d4244529e54"}, "reference_source|ref": {"src": "hda", "id": "c44ebe180a3cd193"}, "reference_source|ref_selector": "history", "call_control|source_qual|use_src_qual|def_nm_q": "40", "call_control|source_qual|use_src_qual|ign_vcf": {"src": "hda", "id": "637c8f59564f151c"}, "call_control|source_qual|use_src_qual|src_qual": "--src-qual", "call_control|set_call_options": "yes"}, "job": {"model_class": "Job", "id": "79f2482c2f958fd9", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:34:57.205942", "create_time": "2023-10-26T14:32:52.216623", "galaxy_version": "21.09", "command_version": "2.1.5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "history_id": "c71426eac153eb4f", "external_id": "gxy-jdbqj", "command_line": "ln -s '/galaxy/server/database/objects/8/c/6/dataset_8c6d246e-ce06-4ff8-b45f-e98bbddd84f1.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/2/7/8/dataset_2783770f-1373-4fe5-bfc1-cfe2632982fc.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/3/e/8/metadata_3e86f55f-9938-472d-8219-e403edc00300.dat' reads.bam.bai && ln -s '/galaxy/server/database/objects/c/c/7/dataset_cc7ae7bb-8a28-466c-90c3-61a76c62c5b4.dat' ign0.vcf && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf 'ign0.vcf' --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 2, \"bonf\": \"dynamic\", \"filter_type\": \"set_lofreq_standard\", \"others\": \"\", \"sig\": \"0.01\"}", "call_control": "{\"__current_case__\": 1, \"align_quals\": {\"alnqual\": {\"__current_case__\": 0, \"alnqual_choice\": {\"__current_case__\": 1, \"alnquals_to_use\": \"\", \"extended_baq\": \"true\"}, \"use_alnqual\": \"\"}}, \"bc_quals\": {\"alt_bq\": {\"__current_case__\": 0, \"modify\": \"\"}, \"min_alt_bq\": \"6\", \"min_bq\": \"6\"}, \"coverage\": {\"max_depth\": \"1000000\", \"min_cov\": \"1\"}, \"joint_qual\": {\"def_alt_jq\": \"0\", \"min_alt_jq\": \"0\", \"min_jq\": \"0\"}, \"map_quals\": {\"min_mq\": \"0\", \"use_mq\": {\"__current_case__\": 0, \"max_mq\": \"255\", \"no_mq\": \"\"}}, \"pe\": {\"use_orphan\": \"false\"}, \"set_call_options\": \"yes\", \"source_qual\": {\"use_src_qual\": {\"__current_case__\": 1, \"def_nm_q\": \"40\", \"ign_vcf\": {\"values\": [{\"id\": 265, \"src\": \"hda\"}]}, \"src_qual\": \"--src-qual\"}}}", "variant_types": "\"\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 264, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "2eda2d4244529e54", "src": "hda", "uuid": "2783770f-1373-4fe5-bfc1-cfe2632982fc"}, "ref": {"id": "c44ebe180a3cd193", "src": "hda", "uuid": "8c6d246e-ce06-4ff8-b45f-e98bbddd84f1"}, "call_control|source_qual|ign_vcf": {"id": "637c8f59564f151c", "src": "hda", "uuid": "cc7ae7bb-8a28-466c-90c3-61a76c62c5b4"}}, "outputs": {"variants": {"id": "ea486baae2c2d08d", "src": "hda", "uuid": "453c63f8-c577-4e20-ba4c-9eb8103a4aae"}}, "output_collections": {}, "tool_stdout": "INFO [2023-10-26 14:34:45,883]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf ign0.vcf --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2023-10-26 14:34:45,901]: Adding 3 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2023-10-26 14:34:48,112]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/157/tmp/lofreq2_call_parallelg9me6xq2/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "INFO [2023-10-26 14:34:45,883]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf ign0.vcf --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2023-10-26 14:34:45,901]: Adding 3 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2023-10-26 14:34:48,112]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/157/tmp/lofreq2_call_parallelg9me6xq2/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2023-10-26 14:34:48", "plugin": "core", "name": "end_epoch", "raw_value": "1698330888.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:34:45", "plugin": "core", "name": "start_epoch", "raw_value": "1698330885.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "lofreq_call/2.1.5+galaxy2-3", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 3, "time_seconds": 136.41565489768982, "inputs": {"reads": {"src": "hda", "id": "d200b0f6552d77fe"}, "reference_source|ref": {"src": "hda", "id": "4734a144bfb034b5"}, "reference_source|ref_selector": "history", "filter_control|filter_type": "set_all_off"}, "job": {"model_class": "Job", "id": "32b0b0c6002fb73b", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:37:13.742500", "create_time": "2023-10-26T14:35:08.608412", "galaxy_version": "21.09", "command_version": "2.1.5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "history_id": "c71426eac153eb4f", "external_id": "gxy-zjdvr", "command_line": "ln -s '/galaxy/server/database/objects/9/d/a/dataset_9daf726c-57ae-488c-9100-e6eb3adc2b9f.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/2/c/f/dataset_2cfb9d43-b906-49a1-a36b-d3b2fa9b7e52.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/2/a/5/metadata_2a513a69-4911-481a-b583-779536d0fe83.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --sig 1 --bonf 1 --no-default-filter reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && ln -s variants.vcf variants.vcf.gz && gzip -df variants.vcf.gz && echo set_all_off", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 0, \"bonf\": \"1\", \"filter_type\": \"set_all_off\", \"others\": \"--no-default-filter\", \"sig\": \"1\"}", "call_control": "{\"__current_case__\": 0, \"set_call_options\": \"no\"}", "variant_types": "\"\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 268, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "d200b0f6552d77fe", "src": "hda", "uuid": "2cfb9d43-b906-49a1-a36b-d3b2fa9b7e52"}, "ref": {"id": "4734a144bfb034b5", "src": "hda", "uuid": "9daf726c-57ae-488c-9100-e6eb3adc2b9f"}}, "outputs": {"variants": {"id": "b9ce4ef5241127e3", "src": "hda", "uuid": "8bc8907a-a230-4644-b7fa-93d7d3ba2564"}}, "output_collections": {}, "tool_stdout": "INFO [2023-10-26 14:37:02,609]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter reads.bam\n\nINFO [2023-10-26 14:37:02,628]: Adding 3 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2023-10-26 14:37:04,372]: Copying concatenated vcf file to final destination\nset_all_off\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "INFO [2023-10-26 14:37:02,609]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter reads.bam\n\nINFO [2023-10-26 14:37:02,628]: Adding 3 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2023-10-26 14:37:04,372]: Copying concatenated vcf file to final destination\nset_all_off\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2023-10-26 14:37:04", "plugin": "core", "name": "end_epoch", "raw_value": "1698331024.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:37:02", "plugin": "core", "name": "start_epoch", "raw_value": "1698331022.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "lofreq_call/2.1.5+galaxy2-4", "has_data": true, "data": {"tool_id": "lofreq_call", "tool_version": "2.1.5+galaxy2", "test_index": 4, "time_seconds": 135.24252676963806, "inputs": {"reads": {"src": "hda", "id": "830d16f0e444fa0a"}, "reference_source|ref": {"src": "hda", "id": "7549687f5f505c71"}, "reference_source|ref_selector": "history", "variant_types": "--call-indels --only-indels", "filter_control|filter_type": "set_all_off"}, "job": {"model_class": "Job", "id": "ca249ba5f5ee05fa", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T14:39:29.176966", "create_time": "2023-10-26T14:37:24.928877", "galaxy_version": "21.09", "command_version": "2.1.5", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", "history_id": "c71426eac153eb4f", "external_id": "gxy-bl4v4", "command_line": "ln -s '/galaxy/server/database/objects/b/0/3/dataset_b039701f-f55f-4953-a084-3687d30c2efe.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/3/3/7/dataset_33739ba9-9028-481f-910a-86d8d4222c1f.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/8/3/f/metadata_83fe8dd4-5151-4640-8ba4-ddcce4ee9cc3.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && ln -s variants.vcf variants.vcf.gz && gzip -df variants.vcf.gz && echo set_all_off", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_control": "{\"__current_case__\": 0, \"bonf\": \"1\", \"filter_type\": \"set_all_off\", \"others\": \"--no-default-filter\", \"sig\": \"1\"}", "call_control": "{\"__current_case__\": 0, \"set_call_options\": \"no\"}", "variant_types": "\"--call-indels --only-indels\"", "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 271, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reads": {"id": "830d16f0e444fa0a", "src": "hda", "uuid": "33739ba9-9028-481f-910a-86d8d4222c1f"}, "ref": {"id": "7549687f5f505c71", "src": "hda", "uuid": "b039701f-f55f-4953-a084-3687d30c2efe"}}, "outputs": {"variants": {"id": "7f9d2cfca651c900", "src": "hda", "uuid": "ced9ea3b-d572-4c56-90fa-b34e66a0441e"}}, "output_collections": {}, "tool_stdout": "INFO [2023-10-26 14:39:17,596]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter reads.bam\n\nINFO [2023-10-26 14:39:17,618]: Adding 3 commands to mp-pool\nNumber of substitution tests performed: 0\nNumber of indel tests performed: 9\nINFO [2023-10-26 14:39:20,200]: Copying concatenated vcf file to final destination\nset_all_off\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "INFO [2023-10-26 14:39:17,596]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter reads.bam\n\nINFO [2023-10-26 14:39:17,618]: Adding 3 commands to mp-pool\nNumber of substitution tests performed: 0\nNumber of indel tests performed: 9\nINFO [2023-10-26 14:39:20,200]: Copying concatenated vcf file to final destination\nset_all_off\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2023-10-26 14:39:20", "plugin": "core", "name": "end_epoch", "raw_value": "1698331160.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 14:39:17", "plugin": "core", "name": "start_epoch", "raw_value": "1698331157.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "multiqc/1.9+galaxy1-0", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 0, "time_seconds": 211.0150237083435, "inputs": {"results_0|software_cond|input": {"src": "hda", "id": "dc38767513cd650f"}, "results_0|software_cond|software": "cutadapt", "results_1|software_cond|input": [{"src": "hda", "id": "6d8043b2996879c5"}, {"src": "hda", "id": "b947fd2e368bcc6f"}], "results_1|software_cond|software": "fastp", "results_2|software_cond|output_0|type": "data", "results_2|software_cond|output_0|input": [{"src": "hda", "id": "3731ce2f201d61ed"}, {"src": "hda", "id": "3ed15c8d2383f456"}], "results_2|software_cond|software": "fastqc", "results_3|software_cond|input": {"src": "hda", "id": "11cc2ee5637165ad"}, "results_3|software_cond|software": "flexbar", "results_4|software_cond|input": [{"src": "hda", "id": "461ed21bb16a1916"}, {"src": "hda", "id": "c5f1d0cf1114bb01"}, {"src": "hda", "id": "d56f1233bcfe6c7c"}], "results_4|software_cond|software": "slamdunk", "results_5|software_cond|input": {"src": "hda", "id": "25eb409de338ff34"}, "results_5|software_cond|software": "sortmerna", "results_6|software_cond|input": {"src": "hda", "id": "2523e5e08cf2afbf"}, "results_6|software_cond|software": "trimmomatic", "title": "Title of the report", "comment": "Commment for the report", "flat": true, "export": true, "saveLog": true}, "job": {"model_class": "Job", "id": "2523e5e08cf2afbf", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:19:42.715995", "create_time": "2023-10-26T13:17:06.231965", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "history_id": "c71426eac153eb4f", "external_id": "gxy-d5pfd", "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/cutadapt_0 && ln -s '/galaxy/server/database/objects/5/a/e/dataset_5aed4d84-b029-48ed-90c4-48cdc40a1752.dat' 'multiqc_WDir/cutadapt_0/cutadapt_txt.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/cutadapt_txt.txt' && grep -q \"This is cutadapt\" 'multiqc_WDir/cutadapt_0/cutadapt_txt.txt' || die \"'This is cutadapt' or 'You are running cutadapt' not found in the file\" && mkdir multiqc_WDir/fastp_1 && ln -s '/galaxy/server/database/objects/d/f/2/dataset_df20d748-1204-49ee-80a3-95f60a56cb46.dat' 'multiqc_WDir/fastp_1/fastp1_json_txtfastp.json' && grep -q \"report_title\" 'multiqc_WDir/fastp_1/fastp1_json_txtfastp.json' || die \"'report_title' or 'report_title' not found in the file\" && ln -s '/galaxy/server/database/objects/b/4/7/dataset_b4750377-6d18-4b56-9bfe-5678b421100c.dat' 'multiqc_WDir/fastp_1/fastp2_json_txtfastp.json' && grep -q \"report_title\" 'multiqc_WDir/fastp_1/fastp2_json_txtfastp.json' || die \"'report_title' or 'report_title' not found in the file\" && mkdir multiqc_WDir/fastqc_2 && mkdir 'multiqc_WDir/fastqc_2/data_0' && mkdir 'multiqc_WDir/fastqc_2/data_0/file_0' && ln -s '/galaxy/server/database/objects/4/e/2/dataset_4e2d31b1-21ae-44dc-b828-2a6e6ebd0f86.dat' 'multiqc_WDir/fastqc_2/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_2/data_0/file_1' && ln -s '/galaxy/server/database/objects/2/2/4/dataset_22424f8e-73f6-431e-b908-4600f6a5759b.dat' 'multiqc_WDir/fastqc_2/data_0/file_1/fastqc_data.txt' && mkdir multiqc_WDir/flexbar_3 && grep -q 'flexible barcode and adapter removal' /galaxy/server/database/objects/9/a/2/dataset_9a2cf3bd-7a9d-4a7a-a3e3-95994ba171a8.dat || die \"Module 'flexbar: 'flexible barcode and adapter removal' not found in the file 'flexbar_txt'\" && ln -s '/galaxy/server/database/objects/9/a/2/dataset_9a2cf3bd-7a9d-4a7a-a3e3-95994ba171a8.dat' 'multiqc_WDir/flexbar_3/flexbar_txt' && mkdir multiqc_WDir/slamdunk_4 && grep -q '# slamdunk' /galaxy/server/database/objects/e/e/5/dataset_ee52ed2b-cfd0-402a-9557-bc56c5114f78.dat || die \"Module 'slamdunk: '# slamdunk' not found in the file 'slamdunk_summary_txt'\" && ln -s '/galaxy/server/database/objects/e/e/5/dataset_ee52ed2b-cfd0-402a-9557-bc56c5114f78.dat' 'multiqc_WDir/slamdunk_4/slamdunk_summary_txt' && grep -q '# slamdunk' /galaxy/server/database/objects/f/2/b/dataset_f2ba8bb4-b5c1-49ce-8d2d-662f550115cf.dat || die \"Module 'slamdunk: '# slamdunk' not found in the file 'slamdunk_reads1_overallrates_csv'\" && ln -s '/galaxy/server/database/objects/f/2/b/dataset_f2ba8bb4-b5c1-49ce-8d2d-662f550115cf.dat' 'multiqc_WDir/slamdunk_4/slamdunk_reads1_overallrates_csv' && grep -q '# slamdunk' /galaxy/server/database/objects/2/3/c/dataset_23c335a1-8a35-42c1-9901-bdddbc9b4cbe.dat || die \"Module 'slamdunk: '# slamdunk' not found in the file 'slamdunk_reads2_overallrates_csv'\" && ln -s '/galaxy/server/database/objects/2/3/c/dataset_23c335a1-8a35-42c1-9901-bdddbc9b4cbe.dat' 'multiqc_WDir/slamdunk_4/slamdunk_reads2_overallrates_csv' && mkdir multiqc_WDir/sortmerna_5 && grep -q 'Minimal SW score based on E-value' /galaxy/server/database/objects/9/2/5/dataset_925a5dd5-d16d-4e6f-9ba6-b2b2d8bfcff5.dat || die \"Module 'sortmerna: 'Minimal SW score based on E-value' not found in the file 'sortmerna_txt'\" && ln -s '/galaxy/server/database/objects/9/2/5/dataset_925a5dd5-d16d-4e6f-9ba6-b2b2d8bfcff5.dat' 'multiqc_WDir/sortmerna_5/sortmerna_txt' && mkdir multiqc_WDir/trimmomatic_6 && grep -q 'Trimmomatic' /galaxy/server/database/objects/0/c/b/dataset_0cb1e9a1-28bd-4bfc-abfa-1d0927849961.dat || die \"Module 'trimmomatic: 'Trimmomatic' not found in the file 'trimmomatic_txt'\" && ln -s '/galaxy/server/database/objects/0/c/b/dataset_0cb1e9a1-28bd-4bfc-abfa-1d0927849961.dat' 'multiqc_WDir/trimmomatic_6/trimmomatic_txt' && multiqc multiqc_WDir --filename \"report\" --title \"Title of the report\" --comment \"Commment for the report\" --flat --export", "traceback": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "\"true\"", "export": "\"true\"", "flat": "\"true\"", "comment": "\"Commment for the report\"", "title": "\"Title of the report\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 5, \"input\": {\"values\": [{\"id\": 34, \"src\": \"hda\"}]}, \"software\": \"cutadapt\"}}, {\"__index__\": 1, \"software_cond\": {\"__current_case__\": 7, \"input\": {\"values\": [{\"id\": 35, \"src\": \"hda\"}, {\"id\": 36, \"src\": \"hda\"}]}, \"software\": \"fastp\"}}, {\"__index__\": 2, \"software_cond\": {\"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 37, \"src\": \"hda\"}, {\"id\": 38, \"src\": \"hda\"}]}, \"type\": \"data\"}], \"software\": \"fastqc\"}}, {\"__index__\": 3, \"software_cond\": {\"__current_case__\": 10, \"input\": {\"values\": [{\"id\": 39, \"src\": \"hda\"}]}, \"software\": \"flexbar\"}}, {\"__index__\": 4, \"software_cond\": {\"__current_case__\": 25, \"input\": {\"values\": [{\"id\": 40, \"src\": \"hda\"}, {\"id\": 41, \"src\": \"hda\"}, {\"id\": 42, \"src\": \"hda\"}]}, \"software\": \"slamdunk\"}}, {\"__index__\": 5, \"software_cond\": {\"__current_case__\": 27, \"input\": {\"values\": [{\"id\": 43, \"src\": \"hda\"}]}, \"software\": \"sortmerna\"}}, {\"__index__\": 6, \"software_cond\": {\"__current_case__\": 30, \"input\": {\"values\": [{\"id\": 44, \"src\": \"hda\"}]}, \"software\": \"trimmomatic\"}}]"}, "inputs": {"results_0|input": {"id": "dc38767513cd650f", "src": "hda", "uuid": "5aed4d84-b029-48ed-90c4-48cdc40a1752"}, "results_1|input": {"id": "6d8043b2996879c5", "src": "hda", "uuid": "df20d748-1204-49ee-80a3-95f60a56cb46"}, "results_1|input1": {"id": "6d8043b2996879c5", "src": "hda", "uuid": "df20d748-1204-49ee-80a3-95f60a56cb46"}, "results_1|input2": {"id": "b947fd2e368bcc6f", "src": "hda", "uuid": "b4750377-6d18-4b56-9bfe-5678b421100c"}, "results_4|input": {"id": "461ed21bb16a1916", "src": "hda", "uuid": "ee52ed2b-cfd0-402a-9557-bc56c5114f78"}, "results_4|input1": {"id": "461ed21bb16a1916", "src": "hda", "uuid": "ee52ed2b-cfd0-402a-9557-bc56c5114f78"}, "results_5|input": {"id": "25eb409de338ff34", "src": "hda", "uuid": "925a5dd5-d16d-4e6f-9ba6-b2b2d8bfcff5"}, "results_6|input": {"id": "2523e5e08cf2afbf", "src": "hda", "uuid": "0cb1e9a1-28bd-4bfc-abfa-1d0927849961"}, "results_2|software_cond|output_0|input": {"id": "3731ce2f201d61ed", "src": "hda", "uuid": "4e2d31b1-21ae-44dc-b828-2a6e6ebd0f86"}, "results_2|software_cond|output_0|input1": {"id": "3731ce2f201d61ed", "src": "hda", "uuid": "4e2d31b1-21ae-44dc-b828-2a6e6ebd0f86"}, "results_2|software_cond|output_0|input2": {"id": "3ed15c8d2383f456", "src": "hda", "uuid": "22424f8e-73f6-431e-b908-4600f6a5759b"}, "results_4|input2": {"id": "c5f1d0cf1114bb01", "src": "hda", "uuid": "f2ba8bb4-b5c1-49ce-8d2d-662f550115cf"}, "results_3|input": {"id": "11cc2ee5637165ad", "src": "hda", "uuid": "9a2cf3bd-7a9d-4a7a-a3e3-95994ba171a8"}, "results_4|input3": {"id": "d56f1233bcfe6c7c", "src": "hda", "uuid": "23c335a1-8a35-42c1-9901-bdddbc9b4cbe"}}, "outputs": {"__new_primary_file_stats|trimmomatic__": {"id": "71b7e6bdfae65f0b", "src": "hda", "uuid": "ab7743c0-e105-4b5a-88df-992d09b06505"}, "__new_primary_file_stats|sources__": {"id": "911d27b92608943a", "src": "hda", "uuid": "679f235b-37b5-4df7-9264-47ec4143b965"}, "__new_primary_file_stats|sortmerna__": {"id": "35698db85100e01b", "src": "hda", "uuid": "51683677-c8d3-42f8-b99c-2166b0553ca9"}, "__new_primary_file_stats|slamdunk_readrates_plus__": {"id": "7e610dfec2e3d643", "src": "hda", "uuid": "10e30876-945d-4b27-8752-14a8d815101e"}, "__new_primary_file_stats|slamdunk_readrates_minus__": {"id": "a998a6ac2e9b3266", "src": "hda", "uuid": "c8ebdea7-3891-40c5-97e7-db30c60493a4"}, 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/galaxy/server/database/jobs_directory/000/44/working/multiqc_WDir\n[INFO ] slamdunk : Found 2 reports\n[INFO ] cutadapt : Found 1 reports\n[WARNING] bargraph : Tried to make bar plot, but had no data\n[INFO ] flexbar : Found 1 logs\n[INFO ] trimmomatic : Found 1 logs\n[INFO ] sortmerna : Found 1 logs\n[INFO ] fastp : Found 2 reports\n[INFO ] fastqc : Found 2 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : Plots : report_plots\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stderr": "[WARNING] multiqc : MultiQC Version v1.16 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/44/working/multiqc_WDir\n[INFO ] slamdunk : Found 2 reports\n[INFO ] cutadapt : Found 1 reports\n[WARNING] bargraph : Tried to make bar plot, but had no data\n[INFO ] flexbar : Found 1 logs\n[INFO ] trimmomatic : Found 1 logs\n[INFO ] sortmerna : Found 1 logs\n[INFO ] fastp : Found 2 reports\n[INFO ] fastqc : Found 2 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : Plots : report_plots\n[INFO ] multiqc : MultiQC complete\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "28 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "28.0000000"}, {"title": "Job End Time", "value": "2023-10-26 13:19:29", "plugin": "core", "name": "end_epoch", "raw_value": "1698326369.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:19:01", "plugin": "core", "name": "start_epoch", "raw_value": "1698326341.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "multiqc/1.9+galaxy1-1", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 1, "time_seconds": 191.88426566123962, "inputs": {"results_0|software_cond|output_0|type": "align", "results_0|software_cond|output_0|input": {"src": "hda", "id": "abb201f61576c33c"}, "results_0|software_cond|software": "bismark", "results_1|software_cond|input": [{"src": "hda", "id": "59da53af7ab7fa56"}, {"src": "hda", "id": "8fc4b62330ae1d3f"}], "results_1|software_cond|software": "bowtie2", "results_2|software_cond|input": [{"src": "hda", "id": "5e734a099c54eaab"}, {"src": "hda", "id": "85bbfee00d54840d"}], "results_2|software_cond|software": "hisat2", "results_3|software_cond|input": [{"src": "hda", "id": "30df981bf4b7a4d2"}, {"src": "hda", "id": "30df981bf4b7a4d2"}, {"src": "hda", "id": "b46faf8683e7b0b7"}], "results_3|software_cond|software": "hicexplorer", "results_4|software_cond|input": [{"src": "hda", "id": "006de9e60e364ce6"}, {"src": "hda", "id": "e2a07def78338838"}], "results_4|software_cond|software": "kallisto", "results_5|software_cond|input": [{"src": "hda", "id": "9057ae837e3c79e6"}, {"src": "hda", "id": "f690b1bb7da4813d"}], "results_5|software_cond|software": "macs2", "results_6|software_cond|output_0|type|input": {"src": "hda", "id": "e7f6f11731ee45f6"}, "results_6|software_cond|output_0|type|type": "log", "results_6|software_cond|output_1|type|input": {"src": "hda", "id": "5e3bd1c695c27720"}, "results_6|software_cond|output_1|type|type": "genecounts", "results_6|software_cond|software": "star", "results_7|software_cond|input": {"src": "hda", "id": "219eae171f5809cf"}, "results_7|software_cond|software": "tophat", "saveLog": false}, "job": {"model_class": "Job", "id": "c111bb0a3b38ba73", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:22:55.448515", "create_time": "2023-10-26T13:20:50.601534", "galaxy_version": "21.09", "command_version": "multiqc, version 1.9", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "history_id": "c71426eac153eb4f", "external_id": "gxy-pfnv7", "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/bismark_0 && mkdir 'multiqc_WDir/bismark_0/align_0' && ln -s '/galaxy/server/database/objects/6/a/3/dataset_6a380f41-23ef-492c-8ca5-d435d649613a.dat' 'multiqc_WDir/bismark_0/align_0/bismark_txt_SE_report.txt' && mkdir multiqc_WDir/bowtie2_1 && grep -q '% overall alignment rate' /galaxy/server/database/objects/7/1/f/dataset_71f378ae-5ad7-4243-a8c5-7d4eceb2d14a.dat || die \"Module 'bowtie2: '% overall alignment rate' not found in the file 'bowtie2_1_txt'\" && ln -s '/galaxy/server/database/objects/7/1/f/dataset_71f378ae-5ad7-4243-a8c5-7d4eceb2d14a.dat' 'multiqc_WDir/bowtie2_1/bowtie2_1_txt' && grep -q '% overall alignment rate' /galaxy/server/database/objects/a/5/9/dataset_a594f246-6a81-4fd6-9801-f42e6dd2ddb3.dat || die \"Module 'bowtie2: '% overall alignment rate' not found in the file 'bowtie2_2_txt'\" && ln -s '/galaxy/server/database/objects/a/5/9/dataset_a594f246-6a81-4fd6-9801-f42e6dd2ddb3.dat' 'multiqc_WDir/bowtie2_1/bowtie2_2_txt' && mkdir multiqc_WDir/hisat2_2 && grep -q 'HISAT2 summary stats:' /galaxy/server/database/objects/3/8/b/dataset_38b0ea77-023a-49d4-8bc0-1c8235f7d222.dat || die \"Module 'hisat2: 'HISAT2 summary stats:' not found in the file 'hisat2_1_txt'\" && ln -s '/galaxy/server/database/objects/3/8/b/dataset_38b0ea77-023a-49d4-8bc0-1c8235f7d222.dat' 'multiqc_WDir/hisat2_2/hisat2_1_txt' && grep -q 'HISAT2 summary stats:' /galaxy/server/database/objects/0/1/d/dataset_01de8c48-dcec-4741-afa1-e18a3bf3c151.dat || die \"Module 'hisat2: 'HISAT2 summary stats:' not found in the file 'hisat2_2_txt'\" && ln -s '/galaxy/server/database/objects/0/1/d/dataset_01de8c48-dcec-4741-afa1-e18a3bf3c151.dat' 'multiqc_WDir/hisat2_2/hisat2_2_txt' && mkdir multiqc_WDir/hicexplorer_3 && grep -q 'Min rest. site distance' /galaxy/server/database/objects/f/3/a/dataset_f3a09388-cde3-46b0-bd10-92a2a1b84b02.dat || die \"Module 'hicexplorer: 'Min rest. site distance' not found in the file 'hicexplorer1_log'\" && ln -s '/galaxy/server/database/objects/f/3/a/dataset_f3a09388-cde3-46b0-bd10-92a2a1b84b02.dat' 'multiqc_WDir/hicexplorer_3/hicexplorer1_log' && grep -q 'Min rest. site distance' /galaxy/server/database/objects/f/3/a/dataset_f3a09388-cde3-46b0-bd10-92a2a1b84b02.dat || die \"Module 'hicexplorer: 'Min rest. site distance' not found in the file 'hicexplorer1_log'\" && ln -s '/galaxy/server/database/objects/f/3/a/dataset_f3a09388-cde3-46b0-bd10-92a2a1b84b02.dat' 'multiqc_WDir/hicexplorer_3/hicexplorer1_log_1' && grep -q 'Min rest. site distance' /galaxy/server/database/objects/0/c/e/dataset_0cec1555-608b-461a-9ec2-82028f0315a4.dat || die \"Module 'hicexplorer: 'Min rest. site distance' not found in the file 'hicexplorer2_log'\" && ln -s '/galaxy/server/database/objects/0/c/e/dataset_0cec1555-608b-461a-9ec2-82028f0315a4.dat' 'multiqc_WDir/hicexplorer_3/hicexplorer2_log' && mkdir multiqc_WDir/kallisto_4 && grep -q 'finding pseudoalignments for the reads' /galaxy/server/database/objects/7/1/8/dataset_7185a266-495b-4dc9-8605-98fd5424ed2f.dat || die \"Module 'kallisto: 'finding pseudoalignments for the reads' not found in the file 'kallisto_1_txt'\" && ln -s '/galaxy/server/database/objects/7/1/8/dataset_7185a266-495b-4dc9-8605-98fd5424ed2f.dat' 'multiqc_WDir/kallisto_4/kallisto_1_txt' && grep -q 'finding pseudoalignments for the reads' /galaxy/server/database/objects/a/5/f/dataset_a5f5c1fd-c8af-45aa-998c-fa30da2bc8d5.dat || die \"Module 'kallisto: 'finding pseudoalignments for the reads' not found in the file 'kallisto_2_txt'\" && ln -s '/galaxy/server/database/objects/a/5/f/dataset_a5f5c1fd-c8af-45aa-998c-fa30da2bc8d5.dat' 'multiqc_WDir/kallisto_4/kallisto_2_txt' && mkdir multiqc_WDir/macs2_5 && grep -q \"# This file is generated by MACS\" /galaxy/server/database/objects/7/0/6/dataset_706158c2-1768-479e-8f92-cc7817b6e06c.dat || die \"'# This file is generated by MACS' not found in the file\" && ln -s '/galaxy/server/database/objects/7/0/6/dataset_706158c2-1768-479e-8f92-cc7817b6e06c.dat' 'multiqc_WDir/macs2_5/macs_1_txt_peaks.xls' && grep -q \"# This file is generated by MACS\" /galaxy/server/database/objects/b/6/b/dataset_b6b4a67d-9256-4676-914c-2c069b85514b.dat || die \"'# This file is generated by MACS' not found in the file\" && ln -s '/galaxy/server/database/objects/b/6/b/dataset_b6b4a67d-9256-4676-914c-2c069b85514b.dat' 'multiqc_WDir/macs2_5/macs_2_txt_peaks.xls' && mkdir multiqc_WDir/star_6 && mkdir 'multiqc_WDir/star_6/log_0' && ln -s '/galaxy/server/database/objects/d/0/5/dataset_d05f6aa8-70d5-45f7-b82a-9cba982cb0da.dat' 'multiqc_WDir/star_6/log_0/star_log_txt_Log.final.out' && mkdir 'multiqc_WDir/star_6/genecounts_1' && ln -s '/galaxy/server/database/objects/8/8/7/dataset_88750b21-93e4-4fc6-aba7-d779649661b5.dat' 'multiqc_WDir/star_6/genecounts_1/star_counts_txt_ReadsPerGene.out.tab' && mkdir multiqc_WDir/tophat_7 && ln -s '/galaxy/server/database/objects/f/d/3/dataset_fd3590ea-8dd3-4d54-9c6b-7916ffe6abb2.dat' 'multiqc_WDir/tophat_7/tophat_txtalign_summary.txt' && multiqc multiqc_WDir --filename \"report\"", "traceback": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "\"false\"", "export": "\"false\"", "flat": "\"false\"", "comment": "\"\"", "title": "\"\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 2, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 86, \"src\": \"hda\"}]}, \"type\": \"align\"}], \"software\": \"bismark\"}}, {\"__index__\": 1, \"software_cond\": {\"__current_case__\": 3, \"input\": {\"values\": [{\"id\": 87, \"src\": \"hda\"}, {\"id\": 88, \"src\": \"hda\"}]}, \"software\": \"bowtie2\"}}, {\"__index__\": 2, \"software_cond\": {\"__current_case__\": 13, \"input\": {\"values\": [{\"id\": 89, \"src\": \"hda\"}, {\"id\": 90, \"src\": \"hda\"}]}, \"software\": \"hisat2\"}}, {\"__index__\": 3, \"software_cond\": {\"__current_case__\": 12, \"input\": {\"values\": [{\"id\": 91, \"src\": \"hda\"}, {\"id\": 91, \"src\": \"hda\"}, {\"id\": 92, \"src\": \"hda\"}]}, \"software\": \"hicexplorer\"}}, {\"__index__\": 4, \"software_cond\": {\"__current_case__\": 15, \"input\": {\"values\": [{\"id\": 93, \"src\": \"hda\"}, {\"id\": 94, \"src\": \"hda\"}]}, \"software\": \"kallisto\"}}, {\"__index__\": 5, \"software_cond\": {\"__current_case__\": 16, \"input\": {\"values\": [{\"id\": 95, \"src\": \"hda\"}, {\"id\": 96, \"src\": \"hda\"}]}, \"software\": \"macs2\"}}, {\"__index__\": 6, \"software_cond\": {\"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 97, \"src\": \"hda\"}]}, \"type\": \"log\"}}, {\"__index__\": 1, \"type\": {\"__current_case__\": 1, \"input\": {\"values\": [{\"id\": 98, \"src\": \"hda\"}]}, \"type\": \"genecounts\"}}], \"software\": \"star\"}}, {\"__index__\": 7, \"software_cond\": {\"__current_case__\": 29, \"input\": {\"values\": [{\"id\": 99, \"src\": \"hda\"}]}, \"software\": \"tophat\"}}]"}, "inputs": {"results_0|software_cond|output_0|input": {"id": "abb201f61576c33c", "src": "hda", "uuid": "6a380f41-23ef-492c-8ca5-d435d649613a"}, "results_1|input": {"id": "59da53af7ab7fa56", "src": "hda", "uuid": "71f378ae-5ad7-4243-a8c5-7d4eceb2d14a"}, "results_1|input1": {"id": "59da53af7ab7fa56", "src": "hda", "uuid": "71f378ae-5ad7-4243-a8c5-7d4eceb2d14a"}, "results_1|input2": {"id": "8fc4b62330ae1d3f", "src": "hda", "uuid": 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"__new_primary_file_stats|bismark_alignment__": {"id": "eb2d82e2380dd709", "src": "hda", "uuid": "4a76e8dd-b18e-409d-b6e0-1fda3f7dddae"}, "__new_primary_file_stats|bowtie2__": {"id": "6098710c9927523e", "src": "hda", "uuid": "be5b7a78-2ab8-48e4-904d-f715a545a7b8"}, "__new_primary_file_stats|cutadapt__": {"id": "e70a6bc426535d9b", "src": "hda", "uuid": "283db258-bca4-4439-b1f8-ce8ea2080173"}, "__new_primary_file_stats|general_stats__": {"id": "a6b23e02efea9856", "src": "hda", "uuid": "28bd17d8-b8e2-4e30-9ab8-841a05f997d6"}, "__new_primary_file_stats|hicexplorer__": {"id": "9c5ed08a27e4280a", "src": "hda", "uuid": "7f8bd0e4-709a-4a8b-9701-4349fe923c0a"}, "__new_primary_file_stats|hisat2__": {"id": "1f4c83493551fed8", "src": "hda", "uuid": "a2e26bbf-d8f3-46f6-a16e-4b5274e91286"}, "__new_primary_file_stats|kallisto__": {"id": "0322da526611af5e", "src": "hda", "uuid": "5e22468d-d7b0-4010-b049-732ccbfdf29c"}, "__new_primary_file_stats|macs__": {"id": "d18f15660bce3c44", "src": "hda", "uuid": 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reports\n[INFO ] tophat : Found 1 reports\n[INFO ] bowtie2 : Found 2 reports\n[INFO ] cutadapt : Found 4 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stderr": "[WARNING] multiqc : MultiQC Version v1.16 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/59/working/multiqc_WDir\n[INFO ] macs2 : Found 2 logs\n[INFO ] bismark : Found 1 alignment reports\n[INFO ] hicexplorer : Found 3 reports\n[INFO ] kallisto : Found 2 reports\n[INFO ] star : Found 1 reports and 1 gene count files\n[INFO ] hisat2 : Found 2 reports\n[INFO ] tophat : Found 1 reports\n[INFO ] bowtie2 : Found 2 reports\n[INFO ] cutadapt : Found 4 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2023-10-26 13:22:45", "plugin": "core", "name": "end_epoch", "raw_value": "1698326565.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:22:40", "plugin": "core", "name": "start_epoch", "raw_value": "1698326560.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "multiqc/1.9+galaxy1-2", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 2, "time_seconds": 268.2890181541443, "inputs": 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"results_3|software_cond|output_4|type": "plotEnrichment", "results_3|software_cond|output_4|input": {"src": "hda", "id": "aed1dd285d3a92db"}, "results_3|software_cond|output_5|type": "plotFingerprintOutRawCounts", "results_3|software_cond|output_5|input": {"src": "hda", "id": "c4c146f740b4d349"}, "results_3|software_cond|software": "deeptools", "results_4|software_cond|input": {"src": "hda", "id": "0a5d5e53b8d558d3"}, "results_4|software_cond|software": "featureCounts", "results_5|software_cond|output_0|type": "base_recalibrator", "results_5|software_cond|output_0|input": {"src": "hda", "id": "c74177a807131b4d"}, "results_5|software_cond|output_1|type": "varianteval", "results_5|software_cond|output_1|input": {"src": "hda", "id": "12b7da2e48f38389"}, "results_5|software_cond|software": "gatk", "results_6|software_cond|input": {"src": "hda", "id": "5cece68cf1f4d96b"}, "results_6|software_cond|software": "htseq", "results_7|software_cond|output_0|type": "gcbias", "results_7|software_cond|output_0|input": {"src": "hda", "id": "a41ca243681c3a54"}, "results_7|software_cond|output_1|type": "insertsize", "results_7|software_cond|output_1|input": {"src": "hda", "id": "cf7ff2ac77061d35"}, "results_7|software_cond|output_2|type": "markdups", "results_7|software_cond|output_2|input": {"src": "hda", "id": "e5ab228a8838c554"}, "results_7|software_cond|output_3|type": "basedistributionbycycle", "results_7|software_cond|output_3|input": {"src": "hda", "id": "9ead0956dd529287"}, "results_7|software_cond|output_4|type": "rnaseqmetrics", "results_7|software_cond|output_4|input": {"src": "hda", "id": "f548a3df6e50b3b1"}, "results_7|software_cond|output_5|type": "alignment_metrics", "results_7|software_cond|output_5|input": {"src": "hda", "id": "660d59b318f9a0dc"}, "results_7|software_cond|software": "picard", "results_8|software_cond|input": [{"src": "hda", "id": "12fb27312849bef6"}, {"src": "hda", "id": "669c2de77c336dfa"}], "results_8|software_cond|software": "prokka", "results_9|software_cond|input": {"src": "hda", "id": "a7b5f00fb651ace4"}, "results_9|software_cond|software": "qualimap", "results_10|software_cond|input": {"src": "hda", "id": "8bea4c001a3c342f"}, "results_10|software_cond|software": "quast", "results_11|software_cond|output_0|type|input": {"src": "hda", "id": "a8725b3e92606155"}, "results_11|software_cond|output_0|type|type": "read_gc", "results_11|software_cond|software": "rseqc", "results_12|software_cond|input": {"src": "hda", "id": "3c0634b2a4a02760"}, "results_12|software_cond|software": "samblaster", "results_13|software_cond|output_0|type|input": {"src": "hda", "id": "4b5e36d798842f28"}, "results_13|software_cond|output_0|type|type": "stats", "results_13|software_cond|output_1|type|input": {"src": "hda", "id": "9ac99b62f6c491b1"}, "results_13|software_cond|output_1|type|type": "flagstat", "results_13|software_cond|output_2|type|input": {"src": "hda", "id": "37c6c4b0faf02a87"}, "results_13|software_cond|output_2|type|type": "idxstats", "results_13|software_cond|software": "samtools", "results_14|software_cond|input": {"src": "hda", "id": "7e23d4b98cae94e7"}, "results_14|software_cond|software": "snpeff", "results_15|software_cond|output_0|type|input": {"src": "hda", "id": "75a31f378b64f3bc"}, "results_15|software_cond|output_0|type|type": "tstv_by_qual", "results_15|software_cond|software": "vcftools"}, "job": {"model_class": "Job", "id": "85bbfee00d54840d", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:27:22.988654", "create_time": "2023-10-26T13:25:18.375431", "galaxy_version": "21.09", "command_version": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "history_id": "c71426eac153eb4f", "external_id": "gxy-dzsgn", "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/bamtools_0 && grep -q 'Stats for BAM file(s)' /galaxy/server/database/objects/1/8/f/dataset_18f9ba86-beb7-4cd1-a2ef-485c8816588f.dat || die \"Module 'bamtools: 'Stats for BAM file(s)' not found in the file 'bamtools_txt'\" && ln -s '/galaxy/server/database/objects/1/8/f/dataset_18f9ba86-beb7-4cd1-a2ef-485c8816588f.dat' 'multiqc_WDir/bamtools_0/bamtools_txt' && mkdir multiqc_WDir/bcftools_1 && grep -q 'This file was produced by bcftools stats' /galaxy/server/database/objects/b/5/a/dataset_b5a32d23-2ca1-4a7c-8976-3838a502cb95.dat || die \"Module 'bcftools: 'This file was produced by bcftools stats' not found in the file 'bcftools_txt'\" && ln -s '/galaxy/server/database/objects/b/5/a/dataset_b5a32d23-2ca1-4a7c-8976-3838a502cb95.dat' 'multiqc_WDir/bcftools_1/bcftools_txt' && mkdir multiqc_WDir/busco_2 && ln -s '/galaxy/server/database/objects/d/2/a/dataset_d2a9425f-dc78-4339-8c5e-6cad081f20d7.dat' 'multiqc_WDir/busco_2/short_summary_busco_txt' && mkdir multiqc_WDir/deeptools_3 && mkdir 'multiqc_WDir/deeptools_3/bamPEFragmentSize_0' && grep -q 'Frag.' /galaxy/server/database/objects/1/0/5/dataset_10574b5a-47f5-4649-8e59-1a15e8528d52.dat || die \"Module 'deeptools: 'Frag.' not found in the file 'deeptools_bamPEFragmentSize_txt'\" && ln -s '/galaxy/server/database/objects/1/0/5/dataset_10574b5a-47f5-4649-8e59-1a15e8528d52.dat' 'multiqc_WDir/deeptools_3/bamPEFragmentSize_0/deeptools_bamPEFragmentSize_txt' && mkdir 'multiqc_WDir/deeptools_3/estimateReadFiltering_1' && grep -q 'Internally-determined Duplicate' /galaxy/server/database/objects/d/a/a/dataset_daac0191-daf9-48a5-9554-e99b462e8a3b.dat || die \"Module 'deeptools: 'Internally-determined Duplicate' not found in the file 'deeptools_estimateReadFiltering_txt'\" && ln -s '/galaxy/server/database/objects/d/a/a/dataset_daac0191-daf9-48a5-9554-e99b462e8a3b.dat' 'multiqc_WDir/deeptools_3/estimateReadFiltering_1/deeptools_estimateReadFiltering_txt' && mkdir 'multiqc_WDir/deeptools_3/plotCoverageStdout_2' && grep -q 'sample' /galaxy/server/database/objects/3/9/8/dataset_3984346f-25c9-467f-ab92-0681c082aca2.dat || die \"Module 'deeptools: 'sample' not found in the file 'deeptools_plotCoverageStdout_txt'\" && ln -s '/galaxy/server/database/objects/3/9/8/dataset_3984346f-25c9-467f-ab92-0681c082aca2.dat' 'multiqc_WDir/deeptools_3/plotCoverageStdout_2/deeptools_plotCoverageStdout_txt' && mkdir 'multiqc_WDir/deeptools_3/plotCoverageOutRawCounts_3' && grep -q '#plotCoverage --outRawCounts' /galaxy/server/database/objects/a/9/8/dataset_a980ff26-9ec8-4af5-a953-e7ef3e21090e.dat || die \"Module 'deeptools: '#plotCoverage --outRawCounts' not found in the file 'deeptools_plotCoverageOutRawCounts_txt'\" && ln -s '/galaxy/server/database/objects/a/9/8/dataset_a980ff26-9ec8-4af5-a953-e7ef3e21090e.dat' 'multiqc_WDir/deeptools_3/plotCoverageOutRawCounts_3/deeptools_plotCoverageOutRawCounts_txt' && mkdir 'multiqc_WDir/deeptools_3/plotEnrichment_4' && grep -q 'featureReadCount' /galaxy/server/database/objects/f/4/a/dataset_f4a0be2c-6f60-411a-bdf3-252dda4b77fc.dat || die \"Module 'deeptools: 'featureReadCount' not found in the file 'deeptools_plotEnrichment_txt'\" && ln -s '/galaxy/server/database/objects/f/4/a/dataset_f4a0be2c-6f60-411a-bdf3-252dda4b77fc.dat' 'multiqc_WDir/deeptools_3/plotEnrichment_4/deeptools_plotEnrichment_txt' && mkdir 'multiqc_WDir/deeptools_3/plotFingerprintOutRawCounts_5' && grep -q '#plotFingerprint --outRawCounts' /galaxy/server/database/objects/b/4/8/dataset_b48a10d9-97c7-4216-845e-7f2b502cbb21.dat || die \"Module 'deeptools: '#plotFingerprint --outRawCounts' not found in the file 'deeptools_plotFingerprintOutRawCounts_txt'\" && ln -s '/galaxy/server/database/objects/b/4/8/dataset_b48a10d9-97c7-4216-845e-7f2b502cbb21.dat' 'multiqc_WDir/deeptools_3/plotFingerprintOutRawCounts_5/deeptools_plotFingerprintOutRawCounts_txt' && mkdir multiqc_WDir/featureCounts_4 && if grep -qw Status '/galaxy/server/database/objects/6/c/7/dataset_6c70ea13-4dce-4b3f-9391-cf2f9125783c.dat'; then ln -s '/galaxy/server/database/objects/6/c/7/dataset_6c70ea13-4dce-4b3f-9391-cf2f9125783c.dat' 'multiqc_WDir/featureCounts_4/featureCounts_txt.summary'; else echo -e 'Status\\tfeatureCounts_txt' > 'multiqc_WDir/featureCounts_4/featureCounts_txt.summary'; cat '/galaxy/server/database/objects/6/c/7/dataset_6c70ea13-4dce-4b3f-9391-cf2f9125783c.dat' >> 'multiqc_WDir/featureCounts_4/featureCounts_txt.summary'; fi && mkdir multiqc_WDir/gatk_5 && mkdir 'multiqc_WDir/gatk_5/base_recalibrator_0' && grep -q '#:GATKTable:Arguments:Recalibration' /galaxy/server/database/objects/e/d/3/dataset_ed389b48-d820-4347-859a-e4c94adf8707.dat || die \"Module 'gatk: '#:GATKTable:Arguments:Recalibration' not found in the file 'gatk_BaseRecalibrator_txt'\" && ln -s '/galaxy/server/database/objects/e/d/3/dataset_ed389b48-d820-4347-859a-e4c94adf8707.dat' 'multiqc_WDir/gatk_5/base_recalibrator_0/gatk_BaseRecalibrator_txt' && mkdir 'multiqc_WDir/gatk_5/varianteval_1' && grep -q '#:GATKTable:TiTvVariantEvaluator' /galaxy/server/database/objects/a/f/3/dataset_af352c46-1eec-4b7a-8b92-99f8e1d16998.dat || die \"Module 'gatk: '#:GATKTable:TiTvVariantEvaluator' not found in the file 'gatk_varianteval_txt'\" && ln -s '/galaxy/server/database/objects/a/f/3/dataset_af352c46-1eec-4b7a-8b92-99f8e1d16998.dat' 'multiqc_WDir/gatk_5/varianteval_1/gatk_varianteval_txt' && mkdir multiqc_WDir/htseq_6 && grep -q '__too_low_aQual' /galaxy/server/database/objects/c/b/8/dataset_cb872b36-023c-4bd1-b7b6-e294f3008a30.dat || die \"Module 'htseq: '__too_low_aQual' not found in the file 'htseq_txt'\" && ln -s '/galaxy/server/database/objects/c/b/8/dataset_cb872b36-023c-4bd1-b7b6-e294f3008a30.dat' 'multiqc_WDir/htseq_6/htseq_txt' && mkdir multiqc_WDir/picard_7 && mkdir 'multiqc_WDir/picard_7/gcbias_0' && grep -q 'picard.analysis.GcBias' /galaxy/server/database/objects/e/7/5/dataset_e7545823-0626-4eda-8c38-f594f11b9cb1.dat || die \"Module 'picard: 'picard.analysis.GcBias' not found in the file 'picard_collectGcBias_txt'\" && ln -s '/galaxy/server/database/objects/e/7/5/dataset_e7545823-0626-4eda-8c38-f594f11b9cb1.dat' 'multiqc_WDir/picard_7/gcbias_0/picard_collectGcBias_txt' && mkdir 'multiqc_WDir/picard_7/insertsize_1' && grep -q 'picard.analysis.InsertSizeMetrics' /galaxy/server/database/objects/4/4/0/dataset_440b28bd-e723-4149-a6a8-dd4f764f3d2f.dat || die \"Module 'picard: 'picard.analysis.InsertSizeMetrics' not found in the file 'picard_CollectInsertSizeMetrics_txt'\" && ln -s '/galaxy/server/database/objects/4/4/0/dataset_440b28bd-e723-4149-a6a8-dd4f764f3d2f.dat' 'multiqc_WDir/picard_7/insertsize_1/picard_CollectInsertSizeMetrics_txt' && mkdir 'multiqc_WDir/picard_7/markdups_2' && grep -q 'MarkDuplicates' /galaxy/server/database/objects/a/a/c/dataset_aac4e856-ce3c-4d32-aeb0-79c2a50d99d1.dat || die \"Module 'picard: 'MarkDuplicates' not found in the file 'picard_MarkDuplicates_txt'\" && ln -s '/galaxy/server/database/objects/a/a/c/dataset_aac4e856-ce3c-4d32-aeb0-79c2a50d99d1.dat' 'multiqc_WDir/picard_7/markdups_2/picard_MarkDuplicates_txt' && mkdir 'multiqc_WDir/picard_7/basedistributionbycycle_3' && grep -q 'picard.analysis.BaseDistributionByCycleMetrics' /galaxy/server/database/objects/b/3/6/dataset_b36a9299-7dea-4809-a368-6aed8fb2ae69.dat || die \"Module 'picard: 'picard.analysis.BaseDistributionByCycleMetrics' not found in the file 'picard_CollectBaseDistributionByCycle_txt'\" && ln -s '/galaxy/server/database/objects/b/3/6/dataset_b36a9299-7dea-4809-a368-6aed8fb2ae69.dat' 'multiqc_WDir/picard_7/basedistributionbycycle_3/picard_CollectBaseDistributionByCycle_txt' && mkdir 'multiqc_WDir/picard_7/rnaseqmetrics_4' && grep -q 'Collect' /galaxy/server/database/objects/1/c/9/dataset_1c93effb-4159-476f-a511-1d57554ecb94.dat || die \"Module 'picard: 'Collect' not found in the file 'picard_CollectRnaSeqMetrics_txt'\" && ln -s '/galaxy/server/database/objects/1/c/9/dataset_1c93effb-4159-476f-a511-1d57554ecb94.dat' 'multiqc_WDir/picard_7/rnaseqmetrics_4/picard_CollectRnaSeqMetrics_txt' && mkdir 'multiqc_WDir/picard_7/alignment_metrics_5' && grep -q 'picard.analysis.AlignmentSummaryMetrics' /galaxy/server/database/objects/f/6/4/dataset_f64eddc6-912a-4c4f-a6c1-948431d3fac6.dat || die \"Module 'picard: 'picard.analysis.AlignmentSummaryMetrics' not found in the file 'picard_CollectAlignmentSummaryMetrics_txt'\" && ln -s '/galaxy/server/database/objects/f/6/4/dataset_f64eddc6-912a-4c4f-a6c1-948431d3fac6.dat' 'multiqc_WDir/picard_7/alignment_metrics_5/picard_CollectAlignmentSummaryMetrics_txt' && mkdir multiqc_WDir/prokka_8 && grep -q 'contigs:' /galaxy/server/database/objects/f/9/0/dataset_f90268e1-5aba-4c5d-8765-285c5b08ae1b.dat || die \"Module 'prokka: 'contigs:' not found in the file 'prokka_1_txt'\" && ln -s '/galaxy/server/database/objects/f/9/0/dataset_f90268e1-5aba-4c5d-8765-285c5b08ae1b.dat' 'multiqc_WDir/prokka_8/prokka_1_txt' && grep -q 'contigs:' /galaxy/server/database/objects/5/e/7/dataset_5e7ae7ba-ed2b-411e-b733-d474ff5ad7c0.dat || die \"Module 'prokka: 'contigs:' not found in the file 'prokka_2_txt'\" && ln -s '/galaxy/server/database/objects/5/e/7/dataset_5e7ae7ba-ed2b-411e-b733-d474ff5ad7c0.dat' 'multiqc_WDir/prokka_8/prokka_2_txt' && mkdir multiqc_WDir/qualimap_9 && sample=\"$(grep 'bam file = ' /galaxy/server/database/objects/f/2/4/dataset_f246d831-7d15-430a-9714-4c485b438093.dat | sed 's/bam file = //g' | sed 's: ::g')\" && dir_name=\"multiqc_WDir/qualimap_9/${sample}\" && mkdir -p ${dir_name} && filepath_1=\"${dir_name}/genome_results.txt\" && ln -sf '/galaxy/server/database/objects/f/2/4/dataset_f246d831-7d15-430a-9714-4c485b438093.dat' ${filepath_1} && mkdir multiqc_WDir/quast_10 && mkdir 'multiqc_WDir/quast_10/file_0' && ln -s '/galaxy/server/database/objects/d/e/d/dataset_ded74870-7501-4bc9-b695-d84afa802d3a.dat' 'multiqc_WDir/quast_10/file_0/report.tsv' && mkdir multiqc_WDir/rseqc_11 && mkdir 'multiqc_WDir/rseqc_11/read_gc_0' && ln -s '/galaxy/server/database/objects/1/4/d/dataset_14dd9755-c976-475c-8463-f937fb8f52fe.dat' 'multiqc_WDir/rseqc_11/read_gc_0/file_0.GC.xls' && mkdir multiqc_WDir/samblaster_12 && grep -q 'samblaster: Version' /galaxy/server/database/objects/0/2/8/dataset_0284a575-a709-4094-9bbf-78076d7ac202.dat || die \"Module 'samblaster: 'samblaster: Version' not found in the file 'samblaster_txt'\" && ln -s '/galaxy/server/database/objects/0/2/8/dataset_0284a575-a709-4094-9bbf-78076d7ac202.dat' 'multiqc_WDir/samblaster_12/samblaster_txt' && mkdir multiqc_WDir/samtools_13 && mkdir 'multiqc_WDir/samtools_13/stats_0' && grep -q 'This file was produced by samtools stats' /galaxy/server/database/objects/5/4/8/dataset_5486c7d5-e940-43f1-b906-247fcfec9766.dat || die \"Module 'samtools: 'This file was produced by samtools stats' not found in the file 'samtools_stats_txt'\" && ln -s '/galaxy/server/database/objects/5/4/8/dataset_5486c7d5-e940-43f1-b906-247fcfec9766.dat' 'multiqc_WDir/samtools_13/stats_0/samtools_stats_txt' && mkdir 'multiqc_WDir/samtools_13/flagstat_1' && grep -q 'in total (QC-passed reads + QC-failed reads)' /galaxy/server/database/objects/4/4/c/dataset_44cc52d3-2756-4227-8dbe-e6f9a87d2dc0.dat || die \"Module 'samtools: 'in total (QC-passed reads + QC-failed reads)' not found in the file 'samtools_flagstat_txt'\" && ln -s '/galaxy/server/database/objects/4/4/c/dataset_44cc52d3-2756-4227-8dbe-e6f9a87d2dc0.dat' 'multiqc_WDir/samtools_13/flagstat_1/samtools_flagstat_txt' && mkdir 'multiqc_WDir/samtools_13/idxstats_2' && ln -s '/galaxy/server/database/objects/7/3/1/dataset_7312fd89-bf09-427b-9a11-b7841542d78f.dat' 'multiqc_WDir/samtools_13/idxstats_2/samtools_idxstats_txt_idxstat' && mkdir multiqc_WDir/snpeff_14 && grep -q 'SnpEff_version' /galaxy/server/database/objects/0/c/1/dataset_0c1ecb05-b7dc-429d-8011-210aa58556d0.dat || die \"Module 'snpeff: 'SnpEff_version' not found in the file 'snpeff_csv'\" && ln -s '/galaxy/server/database/objects/0/c/1/dataset_0c1ecb05-b7dc-429d-8011-210aa58556d0.dat' 'multiqc_WDir/snpeff_14/snpeff_csv' && mkdir multiqc_WDir/vcftools_15 && mkdir 'multiqc_WDir/vcftools_15/tstv_by_qual_0' && multiqc multiqc_WDir --filename \"report\"", "traceback": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "\"false\"", "export": "\"false\"", "flat": "\"false\"", "comment": "\"\"", "title": "\"\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 112, \"src\": \"hda\"}]}, \"software\": \"bamtools\"}}, {\"__index__\": 1, \"software_cond\": {\"__current_case__\": 1, \"input\": {\"values\": [{\"id\": 113, \"src\": \"hda\"}]}, \"software\": \"bcftools\"}}, {\"__index__\": 2, \"software_cond\": {\"__current_case__\": 4, \"input\": {\"values\": [{\"id\": 114, \"src\": \"hda\"}]}, \"software\": \"busco\"}}, {\"__index__\": 3, \"software_cond\": {\"__current_case__\": 6, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 115, \"src\": \"hda\"}]}, \"type\": \"bamPEFragmentSize\"}, {\"__index__\": 1, \"input\": {\"values\": [{\"id\": 116, \"src\": \"hda\"}]}, \"type\": \"estimateReadFiltering\"}, {\"__index__\": 2, \"input\": {\"values\": [{\"id\": 117, \"src\": \"hda\"}]}, \"type\": \"plotCoverageStdout\"}, {\"__index__\": 3, \"input\": {\"values\": [{\"id\": 118, \"src\": \"hda\"}]}, \"type\": \"plotCoverageOutRawCounts\"}, {\"__index__\": 4, \"input\": {\"values\": [{\"id\": 119, \"src\": \"hda\"}]}, \"type\": \"plotEnrichment\"}, {\"__index__\": 5, \"input\": {\"values\": [{\"id\": 120, \"src\": \"hda\"}]}, \"type\": \"plotFingerprintOutRawCounts\"}], \"software\": \"deeptools\"}}, {\"__index__\": 4, \"software_cond\": {\"__current_case__\": 9, \"input\": {\"values\": [{\"id\": 121, \"src\": \"hda\"}]}, \"software\": \"featureCounts\"}}, {\"__index__\": 5, \"software_cond\": {\"__current_case__\": 11, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 122, \"src\": \"hda\"}]}, \"type\": \"base_recalibrator\"}, {\"__index__\": 1, \"input\": {\"values\": [{\"id\": 123, \"src\": \"hda\"}]}, \"type\": \"varianteval\"}], \"software\": \"gatk\"}}, {\"__index__\": 6, \"software_cond\": {\"__current_case__\": 14, \"input\": {\"values\": [{\"id\": 124, \"src\": \"hda\"}]}, \"software\": \"htseq\"}}, {\"__index__\": 7, \"software_cond\": {\"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 125, \"src\": \"hda\"}]}, \"type\": \"gcbias\"}, {\"__index__\": 1, \"input\": {\"values\": [{\"id\": 126, \"src\": \"hda\"}]}, \"type\": \"insertsize\"}, {\"__index__\": 2, \"input\": {\"values\": [{\"id\": 127, \"src\": \"hda\"}]}, \"type\": 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reports\n[INFO ] samtools : Found 1 stats reports\n[INFO ] samtools : Found 1 flagstat reports\n[INFO ] samtools : Found 1 idxstats reports\n[INFO ] bamtools : Found 1 bamtools stats reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "7 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "7.0000000"}, {"title": "Job End Time", "value": "2023-10-26 13:27:12", "plugin": "core", "name": "end_epoch", "raw_value": "1698326832.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:27:05", "plugin": "core", "name": "start_epoch", "raw_value": "1698326825.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores 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"tool_stderr": "[WARNING] multiqc : MultiQC Version v1.16 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/93/working/multiqc_WDir\n[INFO ] custom_content : section_0: Found 2 samples (linegraph)\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stderr": "[WARNING] multiqc : MultiQC Version v1.16 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/93/working/multiqc_WDir\n[INFO ] custom_content : section_0: Found 2 samples (linegraph)\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "stdout": 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"job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2023-10-26 13:29:31", "plugin": "core", "name": "end_epoch", "raw_value": "1698326971.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:29:28", "plugin": "core", "name": "start_epoch", "raw_value": "1698326968.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output html_report: Test output file (report_manual_custom_content.html) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "multiqc/1.9+galaxy1-4", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 4, "time_seconds": 137.28190231323242, "inputs": {"results_0|software_cond|output_0|type": "data", "results_0|software_cond|output_0|input": [{"src": "hda", "id": "06fb0650b192de35"}, {"src": "hda", "id": "6eff9dee9707d390"}], "results_0|software_cond|software": "fastqc", "title": "Title of the report", "comment": "Commment for the report", "flat": true, "export": true}, "job": {"model_class": "Job", "id": "f690b1bb7da4813d", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:31:57.587526", "create_time": "2023-10-26T13:29:52.657049", "galaxy_version": "21.09", "command_version": "multiqc, version 1.9", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "history_id": "c71426eac153eb4f", "external_id": "gxy-ln2v6", "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/fastqc_0 && mkdir 'multiqc_WDir/fastqc_0/data_0' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/galaxy/server/database/objects/f/9/e/dataset_f9efd93a-7d64-4492-bfb1-e6520dc67910.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/galaxy/server/database/objects/3/f/e/dataset_3fe77c19-d680-4076-a7fc-7889ef0364ae.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' && multiqc multiqc_WDir --filename \"report\" --title \"Title of the report\" --comment \"Commment for the report\" --flat --export", "traceback": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "\"false\"", "export": "\"true\"", "flat": "\"true\"", "comment": "\"Commment for the report\"", "title": "\"Title of the report\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 168, \"src\": \"hda\"}, {\"id\": 169, \"src\": \"hda\"}]}, \"type\": \"data\"}], \"software\": \"fastqc\"}}]"}, "inputs": {"results_0|software_cond|output_0|input": {"id": "06fb0650b192de35", "src": "hda", "uuid": "f9efd93a-7d64-4492-bfb1-e6520dc67910"}, "results_0|software_cond|output_0|input1": {"id": "06fb0650b192de35", "src": "hda", "uuid": "f9efd93a-7d64-4492-bfb1-e6520dc67910"}, "results_0|software_cond|output_0|input2": {"id": "6eff9dee9707d390", "src": "hda", "uuid": "3fe77c19-d680-4076-a7fc-7889ef0364ae"}}, "outputs": {"html_report": {"id": "40391639e3739056", "src": "hda", "uuid": "0a904a46-b2de-4ffe-b548-9649e4ada177"}, "__new_primary_file_plots|fastqc_per_base_n_content_plot_1__": {"id": "25e5b19bc7c5364b", "src": "hda", "uuid": "aad9063f-88f6-4d0b-a9ed-6fcfe6d53bbc"}, "__new_primary_file_plots|fastqc_per_base_sequence_quality_plot_1__": {"id": "1d2949cf4728f2cf", 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Found 1 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stderr": "[WARNING] multiqc : MultiQC Version v1.16 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/98/working/multiqc_WDir\n[INFO ] pycoqc : Found 1 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2023-10-26 13:34:00", 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FirstName,LastName,sum(t2.c3) as \"TotalSales\" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;\n ", "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": "2023-10-26 12:49:37", "plugin": "core", "name": "end_epoch", "raw_value": "1698324577.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 12:49:37", "plugin": "core", "name": "start_epoch", "raw_value": "1698324577.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "query_tabular/3.3.0-10", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 10, "time_seconds": 129.142413854599, "inputs": {"tables_0|table": {"src": "hda", "id": "d66fe2f3d95e398c"}, "tables_0|input_opts|linefilters_0|filter|regex_pattern": "NOT TO BE FOUND", "tables_0|input_opts|linefilters_0|filter|regex_action": "include_find", "tables_0|input_opts|linefilters_0|filter|filter_type": "regex", "tables_0|tbl_opts|table_name": "epitope", "tables_0|tbl_opts|column_names_from_first_line": false, "tables_0|tbl_opts|col_names": "pos,peptide,logscore,,,,Allele", "sqlquery": "SELECT pos,peptide,logscore,Allele FROM epitope", "query_result|header_prefix": "", "query_result|header": "yes"}, "job": {"model_class": "Job", "id": "d66fe2f3d95e398c", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:09:36.390581", "create_time": "2023-10-26T13:07:37.977782", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "c71426eac153eb4f", "external_id": "gxy-knl54", "command_line": "cat '/galaxy/server/database/jobs_directory/000/26/configs/tmpdeiie3y1' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/26/configs/tmpqnzpmena' -Q '/galaxy/server/database/jobs_directory/000/26/configs/tmpdeiie3y1' -o '/galaxy/server/database/objects/7/3/d/dataset_73df267e-081e-47fb-9212-c854869f306a.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}", "sqlquery": "\"SELECT pos,peptide,logscore,Allele FROM epitope\"", "save_db": "\"false\"", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"NOT TO BE FOUND\"}}]}, \"table\": {\"values\": [{\"id\": 26, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"pos,peptide,logscore,,,,Allele\", \"column_names_from_first_line\": \"false\", \"indexes\": [], \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"table_name\": \"epitope\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "d66fe2f3d95e398c", "src": "hda", "uuid": "62059442-02c1-4c50-a5c6-026d3c03cc5b"}}, "outputs": {"output": {"id": "ecde2be37cbd4624", "src": "hda", "uuid": "73df267e-081e-47fb-9212-c854869f306a"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "\nSELECT pos,peptide,logscore,Allele FROM epitope\n ", "job_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/6/2/0/dataset_62059442-02c1-4c50-a5c6-026d3c03cc5b.dat', 'table_name': 'epitope', 'column_names': 'pos,peptide,logscore,,,,Allele', 'filters': [{'filter': 'regex', 'pattern': 'NOT TO BE FOUND', 'action': 'include_find'}]}]}\n\nSQL: \nSELECT pos,peptide,logscore,Allele FROM epitope\n \nrowcount: None\n", "stderr": "\nJSON: {'tables': [{'file_path': '/galaxy/server/database/objects/6/2/0/dataset_62059442-02c1-4c50-a5c6-026d3c03cc5b.dat', 'table_name': 'epitope', 'column_names': 'pos,peptide,logscore,,,,Allele', 'filters': [{'filter': 'regex', 'pattern': 'NOT TO BE FOUND', 'action': 'include_find'}]}]}\n\nSQL: \nSELECT pos,peptide,logscore,Allele FROM epitope\n \nrowcount: None\n", "stdout": "\n\nSELECT pos,peptide,logscore,Allele FROM epitope\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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:09:26", "plugin": "core", "name": "start_epoch", "raw_value": "1698325766.0000000"}, {"title": "Job End Time", "value": "2023-10-26 13:09:26", "plugin": "core", "name": "end_epoch", "raw_value": "1698325766.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "query_tabular/3.3.0-11", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 11, "time_seconds": 130.20933389663696, "inputs": {"tables_0|table": {"src": "hda", "id": "b233ece78161fde8"}, "sqlquery": "SELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1"}, "job": {"model_class": "Job", "id": "b233ece78161fde8", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:11:46.661986", "create_time": "2023-10-26T13:09:47.822278", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "c71426eac153eb4f", "external_id": "gxy-q8b2p", "command_line": "cat '/galaxy/server/database/jobs_directory/000/28/configs/tmp16bl6jlt' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/28/configs/tmpyg44wke8' -Q '/galaxy/server/database/jobs_directory/000/28/configs/tmp16bl6jlt' --comment_char='#' -o '/galaxy/server/database/objects/e/1/2/dataset_e124e886-2c2d-4d4d-9011-463d3e70c881.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"SELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\"", "save_db": "\"false\"", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": []}, \"table\": {\"values\": [{\"id\": 28, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"\", \"column_names_from_first_line\": \"false\", \"indexes\": [], \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"table_name\": \"\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "b233ece78161fde8", "src": "hda", "uuid": "70b0bd54-a5dd-4323-8334-b7ba4bf3c4ff"}}, "outputs": {"output": {"id": "737bde765241cdbd", "src": "hda", "uuid": "e124e886-2c2d-4d4d-9011-463d3e70c881"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "\nSELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\n ", "job_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/7/0/b/dataset_70b0bd54-a5dd-4323-8334-b7ba4bf3c4ff.dat', 'table_name': 't1', 'column_names': ''}]}\nsqrt(-2): math domain error\nsqrt(-2.222): math domain error\nlog(-2): math domain error\nlog10(-2): math domain error\nacos(-2): math domain error\nasin(-2): math domain error\nacosh(-2): math domain error\nsqrt(-1): math domain error\nsqrt(-1.999): math domain error\nlog(-1): math domain error\nlog10(-1): math domain error\nacosh(-1): math domain error\nlog(0): math domain error\nlog10(0): math domain error\nacosh(0): math domain error\nacos(2): math domain error\nasin(2): math domain error\nacos(3): math domain error\nasin(3): math domain error\nacos(4): math domain error\nasin(4): math domain error\nacos(5): math domain error\nasin(5): math domain error\n\nSQL: \nSELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\n \nrowcount: None\n", "stderr": "\nJSON: {'tables': [{'file_path': '/galaxy/server/database/objects/7/0/b/dataset_70b0bd54-a5dd-4323-8334-b7ba4bf3c4ff.dat', 'table_name': 't1', 'column_names': ''}]}\nsqrt(-2): math domain error\nsqrt(-2.222): math domain error\nlog(-2): math domain error\nlog10(-2): math domain error\nacos(-2): math domain error\nasin(-2): math domain error\nacosh(-2): math domain error\nsqrt(-1): math domain error\nsqrt(-1.999): math domain error\nlog(-1): math domain error\nlog10(-1): math domain error\nacosh(-1): math domain error\nlog(0): math domain error\nlog10(0): math domain error\nacosh(0): math domain error\nacos(2): math domain error\nasin(2): math domain error\nacos(3): math domain error\nasin(3): math domain error\nacos(4): math domain error\nasin(4): math domain error\nacos(5): math domain error\nasin(5): math domain error\n\nSQL: \nSELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\n \nrowcount: None\n", "stdout": "\n\nSELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1\n ", "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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:11:36", "plugin": "core", "name": "start_epoch", "raw_value": "1698325896.0000000"}, {"title": "Job End Time", "value": "2023-10-26 13:11:36", "plugin": "core", "name": "end_epoch", "raw_value": "1698325896.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "query_tabular/3.3.0-2", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 2, "time_seconds": 131.18615317344666, "inputs": {"tables_0|table": {"src": "hda", "id": "e3e0a50be7ada402"}, "tables_0|input_opts|linefilters_0|filter|skip_lines": "1", "tables_0|input_opts|linefilters_0|filter|filter_type": "skip", "tables_0|tbl_opts|col_names": ",FirstName,LastName,,BirthDate,", "sqlquery": "select FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)"}, "job": {"model_class": "Job", "id": "18923b9324b83db6", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T12:51:58.566499", "create_time": "2023-10-26T12:49:58.281806", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "c71426eac153eb4f", "external_id": "gxy-xxngz", "command_line": "cat '/galaxy/server/database/jobs_directory/000/8/configs/tmpjdhtgp5s' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/8/configs/tmplguc8bih' -Q '/galaxy/server/database/jobs_directory/000/8/configs/tmpjdhtgp5s' --comment_char='#' -o '/galaxy/server/database/objects/4/4/e/dataset_44e6abee-f7ac-4091-be91-9123f7b7d6fa.dat'", "traceback": null, "params": {"workdb": "\"workdb.sqlite\"", "add_to_database": "{\"withdb\": null}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 0, \"filter_type\": \"skip\", \"skip_lines\": \"1\"}}]}, \"table\": {\"values\": [{\"id\": 7, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \",FirstName,LastName,,BirthDate,\", \"column_names_from_first_line\": \"false\", \"indexes\": [], \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"table_name\": \"\"}}]", "modify_database": "{\"sql_stmts\": []}", "save_db": "\"false\"", "sqlquery": "\"select FirstName,LastName,re_sub('^\\\\d{2}(\\\\d{2})-(\\\\d\\\\d)-(\\\\d\\\\d)','\\\\3/\\\\2/\\\\1',BirthDate) as \\\"DOB\\\" from t1 WHERE re_search('[hp]er',c4)\"", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "addqueries": "{\"queries\": []}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"tabular\""}, "inputs": {"tables_0|table": {"id": "e3e0a50be7ada402", "src": "hda", "uuid": "8b34159c-a67c-4d91-8110-ac224532525a"}}, "outputs": {"output": {"id": "18923b9324b83db6", "src": "hda", "uuid": "44e6abee-f7ac-4091-be91-9123f7b7d6fa"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "\nselect FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)\n ", "job_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/8/b/3/dataset_8b34159c-a67c-4d91-8110-ac224532525a.dat', 'table_name': 't1', 'column_names': ',FirstName,LastName,,BirthDate,', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nselect FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)\n \nrowcount: None\n", "stderr": "\nJSON: {'tables': [{'file_path': '/galaxy/server/database/objects/8/b/3/dataset_8b34159c-a67c-4d91-8110-ac224532525a.dat', 'table_name': 't1', 'column_names': ',FirstName,LastName,,BirthDate,', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nselect FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)\n \nrowcount: None\n", "stdout": "\n\nselect FirstName,LastName,re_sub('^\\d{2}(\\d{2})-(\\d\\d)-(\\d\\d)','\\3/\\2/\\1',BirthDate) as \"DOB\" from t1 WHERE re_search('[hp]er',c4)\n ", "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": "2023-10-26 12:51:49", "plugin": "core", "name": "end_epoch", "raw_value": "1698324709.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 12:51:49", "plugin": "core", "name": "start_epoch", "raw_value": "1698324709.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "query_tabular/3.3.0-3", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 3, "time_seconds": 133.3966727256775, "inputs": {"tables_0|table": {"src": "hda", "id": "3488b1fd562001e4"}, "tables_0|input_opts|linefilters_0|filter|comment_char": "35", "tables_0|input_opts|linefilters_0|filter|filter_type": "comment", "tables_0|tbl_opts|table_name": "iedb", "tables_0|tbl_opts|col_names": "ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank", "tables_1|table": {"src": "hda", "id": "60556087a22d15d5"}, "tables_1|input_opts|linefilters_0|filter|skip_lines": "1", "tables_1|input_opts|linefilters_0|filter|filter_type": "skip", "tables_1|tbl_opts|table_name": "mhc_summary", "tables_1|tbl_opts|col_names": "pos,peptide,logscore,affinity,Bind_Level,Protein,Allele", "sqlquery": "select iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank"}, "job": {"model_class": "Job", "id": "5caa2a043e88887d", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T12:54:11.798814", "create_time": "2023-10-26T12:52:11.034864", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "c71426eac153eb4f", "external_id": "gxy-fkg6q", "command_line": "cat '/galaxy/server/database/jobs_directory/000/11/configs/tmplmfz1zp3' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/11/configs/tmpxnm1mugf' -Q '/galaxy/server/database/jobs_directory/000/11/configs/tmplmfz1zp3' --comment_char='#' -o '/galaxy/server/database/objects/5/2/9/dataset_529d19ca-234e-44f2-b854-278ea9cb1782.dat'", "traceback": null, "params": {"workdb": "\"workdb.sqlite\"", "add_to_database": "{\"withdb\": null}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}]}, \"table\": {\"values\": [{\"id\": 9, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank\", \"column_names_from_first_line\": \"false\", \"indexes\": [], \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"table_name\": \"iedb\"}}, {\"__index__\": 1, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 0, \"filter_type\": \"skip\", \"skip_lines\": \"1\"}}]}, \"table\": {\"values\": [{\"id\": 10, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"pos,peptide,logscore,affinity,Bind_Level,Protein,Allele\", \"column_names_from_first_line\": \"false\", \"indexes\": [], \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"table_name\": \"mhc_summary\"}}]", "modify_database": "{\"sql_stmts\": []}", "save_db": "\"false\"", "sqlquery": "\"select iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\"", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "addqueries": "{\"queries\": []}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"tabular\""}, "inputs": {"tables_1|table": {"id": "60556087a22d15d5", "src": "hda", "uuid": "a64b06b9-2ca0-4a48-8f3f-8b37eb71dc8c"}, "tables_0|table": {"id": "3488b1fd562001e4", "src": "hda", "uuid": "9d783276-1ad3-450b-b0ce-8f08d7ab1bc9"}}, "outputs": {"output": {"id": "5caa2a043e88887d", "src": "hda", "uuid": "529d19ca-234e-44f2-b854-278ea9cb1782"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "\nselect iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\n ", "job_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/9/d/7/dataset_9d783276-1ad3-450b-b0ce-8f08d7ab1bc9.dat', 'table_name': 'iedb', 'column_names': 'ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}, {'file_path': '/galaxy/server/database/objects/a/6/4/dataset_a64b06b9-2ca0-4a48-8f3f-8b37eb71dc8c.dat', 'table_name': 'mhc_summary', 'column_names': 'pos,peptide,logscore,affinity,Bind_Level,Protein,Allele', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nselect iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\n \nrowcount: None\n", "stderr": "\nJSON: {'tables': [{'file_path': '/galaxy/server/database/objects/9/d/7/dataset_9d783276-1ad3-450b-b0ce-8f08d7ab1bc9.dat', 'table_name': 'iedb', 'column_names': 'ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank', 'filters': [{'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}]}, {'file_path': '/galaxy/server/database/objects/a/6/4/dataset_a64b06b9-2ca0-4a48-8f3f-8b37eb71dc8c.dat', 'table_name': 'mhc_summary', 'column_names': 'pos,peptide,logscore,affinity,Bind_Level,Protein,Allele', 'filters': [{'filter': 'skip', 'count': 1}]}]}\n\nSQL: \nselect iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\n \nrowcount: None\n", "stdout": "\n\nselect iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank\n ", "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": "2023-10-26 12:54:02", "plugin": "core", "name": "end_epoch", "raw_value": "1698324842.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 12:54:02", "plugin": "core", "name": "start_epoch", "raw_value": "1698324842.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "query_tabular/3.3.0-4", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 4, "time_seconds": 130.2547538280487, "inputs": {"add_to_database|withdb": {"src": "hda", "id": "29afc6d7e5f6b2f8"}, "tables_0|table": {"src": "hda", "id": "22b80c9b255750ba"}, "tables_0|input_opts|linefilters_0|filter|regex_pattern": "^\\d+", "tables_0|input_opts|linefilters_0|filter|regex_action": "include_find", "tables_0|input_opts|linefilters_0|filter|filter_type": "regex", "tables_0|input_opts|linefilters_1|filter|comment_char": "35", "tables_0|input_opts|linefilters_1|filter|filter_type": "comment", "tables_0|input_opts|linefilters_2|filter|filter_type": "append_line_num", "tables_0|input_opts|linefilters_3|filter|columns": "7,2,3,4,1", "tables_0|input_opts|linefilters_3|filter|filter_type": "select_columns", "tables_0|input_opts|linefilters_4|filter|column": "c4", "tables_0|input_opts|linefilters_4|filter|regex_pattern": "(\\d+)/(\\d+)/(\\d+)", "tables_0|input_opts|linefilters_4|filter|regex_replace": "19\\3-\\2-\\1", "tables_0|input_opts|linefilters_4|filter|filter_type": "replace", "tables_0|tbl_opts|table_name": "people", "tables_0|tbl_opts|col_names": "id,first,last,dob,pets", "sqlquery": "SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name"}, "job": {"model_class": "Job", "id": "5e6279a617d6ae2f", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T12:56:22.214602", "create_time": "2023-10-26T12:54:23.454764", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "c71426eac153eb4f", "external_id": "gxy-ftq5r", "command_line": "cat '/galaxy/server/database/jobs_directory/000/14/configs/tmpm54ldkqo' && cp '/galaxy/server/database/objects/0/5/6/dataset_0563d710-cfef-420e-91e3-eab8ccee4ed3.dat' 'workdb.sqlite' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/14/configs/tmpd8mcg386' -Q '/galaxy/server/database/jobs_directory/000/14/configs/tmpm54ldkqo' --comment_char='#' -o '/galaxy/server/database/objects/3/c/b/dataset_3cb7e393-b5c6-41e2-93c0-4d373071f383.dat'", "traceback": null, "params": {"workdb": "\"workdb.sqlite\"", "add_to_database": "{\"withdb\": {\"values\": [{\"id\": 12, \"src\": \"hda\"}]}}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"^\\\\d+\"}}, {\"__index__\": 1, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}, {\"__index__\": 2, \"filter\": {\"__current_case__\": 3, \"filter_type\": \"append_line_num\"}}, {\"__index__\": 3, \"filter\": {\"__current_case__\": 9, \"columns\": \"7,2,3,4,1\", \"filter_type\": \"select_columns\"}}, {\"__index__\": 4, \"filter\": {\"__current_case__\": 11, \"add\": null, \"column\": \"c4\", \"filter_type\": \"replace\", \"regex_pattern\": \"(\\\\d+)/(\\\\d+)/(\\\\d+)\", \"regex_replace\": \"19\\\\3-\\\\2-\\\\1\"}}]}, \"table\": {\"values\": [{\"id\": 13, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"id,first,last,dob,pets\", \"column_names_from_first_line\": \"false\", \"indexes\": [], \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"table_name\": \"people\"}}]", "modify_database": "{\"sql_stmts\": []}", "save_db": "\"false\"", "sqlquery": "\"SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\"", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "addqueries": "{\"queries\": []}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"sqlite\""}, "inputs": {"tables_0|table": {"id": "22b80c9b255750ba", "src": "hda", "uuid": "20abe4d9-7ca4-4fb2-8f66-4056fd88bda8"}, "withdb": {"id": "29afc6d7e5f6b2f8", "src": "hda", "uuid": "0563d710-cfef-420e-91e3-eab8ccee4ed3"}}, "outputs": {"output": {"id": "5e6279a617d6ae2f", "src": "hda", "uuid": "3cb7e393-b5c6-41e2-93c0-4d373071f383"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "\nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n ", "job_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/2/0/a/dataset_20abe4d9-7ca4-4fb2-8f66-4056fd88bda8.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}]}\n\nSQL: \nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n \nrowcount: None\n", "stderr": "\nJSON: {'tables': [{'file_path': '/galaxy/server/database/objects/2/0/a/dataset_20abe4d9-7ca4-4fb2-8f66-4056fd88bda8.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}]}\n\nSQL: \nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\n \nrowcount: None\n", "stdout": "\n\nSELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name\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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 12:56:11", "plugin": "core", "name": "start_epoch", "raw_value": "1698324971.0000000"}, {"title": "Job End Time", "value": "2023-10-26 12:56:11", "plugin": "core", "name": "end_epoch", "raw_value": "1698324971.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "query_tabular/3.3.0-5", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 5, "time_seconds": 134.05940175056458, "inputs": {"tables_0|table": {"src": "hda", "id": "50273a791a33df86"}, "tables_0|input_opts|linefilters_0|filter|regex_pattern": "^\\d+", "tables_0|input_opts|linefilters_0|filter|regex_action": "include_find", "tables_0|input_opts|linefilters_0|filter|filter_type": "regex", "tables_0|input_opts|linefilters_1|filter|comment_char": "35", "tables_0|input_opts|linefilters_1|filter|filter_type": "comment", "tables_0|input_opts|linefilters_2|filter|filter_type": "append_line_num", "tables_0|input_opts|linefilters_3|filter|columns": "7,2,3,4,1", "tables_0|input_opts|linefilters_3|filter|filter_type": "select_columns", "tables_0|input_opts|linefilters_4|filter|column": "c4", "tables_0|input_opts|linefilters_4|filter|regex_pattern": "(\\d+)/(\\d+)/(\\d+)", "tables_0|input_opts|linefilters_4|filter|regex_replace": "19\\3-\\2-\\1", "tables_0|input_opts|linefilters_4|filter|filter_type": "replace", "tables_0|tbl_opts|table_name": "people", "tables_0|tbl_opts|col_names": "id,first,last,dob,pets", "tables_1|table": {"src": "hda", "id": "50273a791a33df86"}, "tables_1|input_opts|linefilters_0|filter|regex_pattern": "^\\d+", "tables_1|input_opts|linefilters_0|filter|regex_action": "include_find", "tables_1|input_opts|linefilters_0|filter|filter_type": "regex", "tables_1|input_opts|linefilters_1|filter|filter_type": "append_line_num", "tables_1|input_opts|linefilters_2|filter|columns": "c7,c5,c6", "tables_1|input_opts|linefilters_2|filter|filter_type": "select_columns", "tables_1|input_opts|linefilters_3|filter|columns": "c2,c3", "tables_1|input_opts|linefilters_3|filter|separator": ",", "tables_1|input_opts|linefilters_3|filter|filter_type": "normalize", "tables_1|tbl_opts|table_name": "pet", "tables_1|tbl_opts|col_names": "id,name,animal", "sqlquery": "SELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'"}, "job": {"model_class": "Job", "id": "a7429ae1f0207f3b", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T12:58:36.472693", "create_time": "2023-10-26T12:56:32.582743", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "c71426eac153eb4f", "external_id": "gxy-qw25n", "command_line": "cat '/galaxy/server/database/jobs_directory/000/16/configs/tmp1ox5_hxf' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/16/configs/tmpv7q30xgq' -Q '/galaxy/server/database/jobs_directory/000/16/configs/tmp1ox5_hxf' --comment_char='#' -o '/galaxy/server/database/objects/e/3/7/dataset_e3791212-3a49-45e5-921f-7d7ec1ef8416.dat'", "traceback": null, "params": {"workdb": "\"workdb.sqlite\"", "add_to_database": "{\"withdb\": null}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"^\\\\d+\"}}, {\"__index__\": 1, \"filter\": {\"__current_case__\": 1, \"comment_char\": \"35\", \"filter_type\": \"comment\"}}, {\"__index__\": 2, \"filter\": {\"__current_case__\": 3, \"filter_type\": \"append_line_num\"}}, {\"__index__\": 3, \"filter\": {\"__current_case__\": 9, \"columns\": \"7,2,3,4,1\", \"filter_type\": \"select_columns\"}}, {\"__index__\": 4, \"filter\": {\"__current_case__\": 11, \"add\": null, \"column\": \"c4\", \"filter_type\": \"replace\", \"regex_pattern\": \"(\\\\d+)/(\\\\d+)/(\\\\d+)\", \"regex_replace\": \"19\\\\3-\\\\2-\\\\1\"}}]}, \"table\": {\"values\": [{\"id\": 15, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"id,first,last,dob,pets\", \"column_names_from_first_line\": \"false\", \"indexes\": [], \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"table_name\": \"people\"}}, {\"__index__\": 1, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"^\\\\d+\"}}, {\"__index__\": 1, \"filter\": {\"__current_case__\": 3, \"filter_type\": \"append_line_num\"}}, {\"__index__\": 2, \"filter\": {\"__current_case__\": 9, \"columns\": \"c7,c5,c6\", \"filter_type\": \"select_columns\"}}, {\"__index__\": 3, \"filter\": {\"__current_case__\": 12, \"columns\": \"c2,c3\", \"filter_type\": \"normalize\", \"separator\": \",\"}}]}, \"table\": {\"values\": [{\"id\": 15, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"id,name,animal\", \"column_names_from_first_line\": \"false\", \"indexes\": [], \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"table_name\": \"pet\"}}]", "modify_database": "{\"sql_stmts\": []}", "save_db": "\"false\"", "sqlquery": "\"SELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'\"", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "addqueries": "{\"queries\": []}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"tabular\""}, "inputs": {"tables_1|table": {"id": "50273a791a33df86", "src": "hda", "uuid": "7c847c0d-b2c2-41d0-8daf-71e78ede5d48"}, "tables_0|table": {"id": "50273a791a33df86", "src": "hda", "uuid": "7c847c0d-b2c2-41d0-8daf-71e78ede5d48"}}, "outputs": {"output": {"id": "a7429ae1f0207f3b", "src": "hda", "uuid": "e3791212-3a49-45e5-921f-7d7ec1ef8416"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "\nSELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'\n ", "job_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/7/c/8/dataset_7c847c0d-b2c2-41d0-8daf-71e78ede5d48.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}, {'file_path': '/galaxy/server/database/objects/7/c/8/dataset_7c847c0d-b2c2-41d0-8daf-71e78ede5d48.dat', 'table_name': 'pet', 'column_names': 'id,name,animal', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 5, 6]}, {'filter': 'normalize', 'columns': [2, 3], 'separator': ','}]}]}\n\nSQL: \nSELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'\n \nrowcount: None\n", "stderr": "\nJSON: {'tables': [{'file_path': '/galaxy/server/database/objects/7/c/8/dataset_7c847c0d-b2c2-41d0-8daf-71e78ede5d48.dat', 'table_name': 'people', 'column_names': 'id,first,last,dob,pets', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'regex', 'pattern': '^(#).*$', 'action': 'exclude_match'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 2, 3, 4, 1]}, {'filter': 'replace', 'column': 4, 'pattern': '(\\\\d+)/(\\\\d+)/(\\\\d+)', 'replace': '19\\\\3-\\\\2-\\\\1'}]}, {'file_path': '/galaxy/server/database/objects/7/c/8/dataset_7c847c0d-b2c2-41d0-8daf-71e78ede5d48.dat', 'table_name': 'pet', 'column_names': 'id,name,animal', 'filters': [{'filter': 'regex', 'pattern': '^\\\\d+', 'action': 'include_find'}, {'filter': 'append_line_num'}, {'filter': 'select_columns', 'columns': [7, 5, 6]}, {'filter': 'normalize', 'columns': [2, 3], 'separator': ','}]}]}\n\nSQL: \nSELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'\n \nrowcount: None\n", "stdout": "\n\nSELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'\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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 12:58:26", "plugin": "core", "name": "start_epoch", "raw_value": "1698325106.0000000"}, {"title": "Job End Time", "value": "2023-10-26 12:58:26", "plugin": "core", "name": "end_epoch", "raw_value": "1698325106.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "query_tabular/3.3.0-6", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 6, "time_seconds": 133.58034110069275, "inputs": {"tables_0|table": {"src": "hda", "id": "83aff621f7459129"}, "tables_0|input_opts|linefilters_0|filter|columns": "1,3,2,6,14,19", "tables_0|input_opts|linefilters_0|filter|filter_type": "select_columns", "tables_0|tbl_opts|table_name": "PSMs", "tables_0|tbl_opts|column_names_from_first_line": true, "tables_0|tbl_opts|col_names": "Scan", "sqlquery": "SELECT * from PSMs", "query_result|header_prefix": "", "query_result|header": "yes"}, "job": {"model_class": "Job", "id": "b94c78b0ea0891bd", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:00:49.880151", "create_time": "2023-10-26T12:58:47.007183", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "c71426eac153eb4f", "external_id": "gxy-v5nf8", "command_line": "cat '/galaxy/server/database/jobs_directory/000/18/configs/tmpp4falyzn' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/18/configs/tmpsrke3nf9' -Q '/galaxy/server/database/jobs_directory/000/18/configs/tmpp4falyzn' -o '/galaxy/server/database/objects/9/6/3/dataset_963c097f-b73d-4b4d-9b17-160adb95b36d.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}", "sqlquery": "\"SELECT * from PSMs\"", "save_db": "\"false\"", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 9, \"columns\": \"1,3,2,6,14,19\", \"filter_type\": \"select_columns\"}}]}, \"table\": {\"values\": [{\"id\": 17, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"Scan\", \"column_names_from_first_line\": \"true\", \"indexes\": [], \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"table_name\": \"PSMs\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "83aff621f7459129", "src": "hda", "uuid": "b00884b2-fc9b-4965-b0ea-50eb54a34035"}}, "outputs": {"output": {"id": "b94c78b0ea0891bd", "src": "hda", "uuid": "963c097f-b73d-4b4d-9b17-160adb95b36d"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "\nSELECT * from PSMs\n ", "job_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/b/0/0/dataset_b00884b2-fc9b-4965-b0ea-50eb54a34035.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'Scan', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19]}]}]}\n\nSQL: \nSELECT * from PSMs\n \nrowcount: None\n", "stderr": "\nJSON: {'tables': [{'file_path': '/galaxy/server/database/objects/b/0/0/dataset_b00884b2-fc9b-4965-b0ea-50eb54a34035.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'Scan', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19]}]}]}\n\nSQL: \nSELECT * from PSMs\n \nrowcount: None\n", "stdout": "\n\nSELECT * from PSMs\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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:00:39", "plugin": "core", "name": "start_epoch", "raw_value": "1698325239.0000000"}, {"title": "Job End Time", "value": "2023-10-26 13:00:39", "plugin": "core", "name": "end_epoch", "raw_value": "1698325239.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "query_tabular/3.3.0-7", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 7, "time_seconds": 131.26038646697998, "inputs": {"tables_0|table": {"src": "hda", "id": "bd7e067537c5244a"}, "tables_0|input_opts|linefilters_0|filter|columns": "1,3,2,6,14,19", "tables_0|input_opts|linefilters_0|filter|filter_type": "select_columns", "tables_0|tbl_opts|table_name": "PSMs", "tables_0|tbl_opts|column_names_from_first_line": true, "tables_0|tbl_opts|col_names": "Scan", "sqlquery": "SELECT Scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\" FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")", "query_result|header_prefix": "", "query_result|header": "yes"}, "job": {"model_class": "Job", "id": "d73e90d8c7b46a8b", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:03:01.202003", "create_time": "2023-10-26T13:01:01.050606", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "c71426eac153eb4f", "external_id": "gxy-qw2bz", "command_line": "cat '/galaxy/server/database/jobs_directory/000/20/configs/tmpcgfpgvvj' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/20/configs/tmp52roi43k' -Q '/galaxy/server/database/jobs_directory/000/20/configs/tmpcgfpgvvj' -o '/galaxy/server/database/objects/b/7/2/dataset_b7264b69-17e3-4220-a9b8-45406864d422.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": []}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}", "sqlquery": "\"SELECT Scan,\\\"m/z\\\", \\\"Precursor m/z Error [ppm]\\\", Sequence, \\\"Protein(s)\\\" FROM PSMs WHERE NOT re_search(', ',\\\"Protein(s)\\\")\"", "save_db": "\"false\"", "modify_database": "{\"sql_stmts\": []}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 9, \"columns\": \"1,3,2,6,14,19\", \"filter_type\": \"select_columns\"}}]}, \"table\": {\"values\": [{\"id\": 19, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"Scan\", \"column_names_from_first_line\": \"true\", \"indexes\": [], \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"table_name\": \"PSMs\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "bd7e067537c5244a", "src": "hda", "uuid": "c4ff2f16-2bdf-4e8f-8499-1943fad5cc58"}}, "outputs": {"output": {"id": "d73e90d8c7b46a8b", "src": "hda", "uuid": "b7264b69-17e3-4220-a9b8-45406864d422"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "\nSELECT Scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\" FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n ", "job_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/c/4/f/dataset_c4ff2f16-2bdf-4e8f-8499-1943fad5cc58.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'Scan', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19]}]}]}\n\nSQL: \nSELECT Scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\" FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n \nrowcount: None\n", "stderr": "\nJSON: {'tables': [{'file_path': '/galaxy/server/database/objects/c/4/f/dataset_c4ff2f16-2bdf-4e8f-8499-1943fad5cc58.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'Scan', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19]}]}]}\n\nSQL: \nSELECT Scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\" FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n \nrowcount: None\n", "stdout": "\n\nSELECT Scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\" FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:02:51", "plugin": "core", "name": "start_epoch", "raw_value": "1698325371.0000000"}, {"title": "Job End Time", "value": "2023-10-26 13:02:51", "plugin": "core", "name": "end_epoch", "raw_value": "1698325371.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "query_tabular/3.3.0-8", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 8, "time_seconds": 134.73141741752625, "inputs": {"tables_0|table": {"src": "hda", "id": "bb1a0f380904e977"}, "tables_0|input_opts|linefilters_0|filter|columns": "1,3,2,6,14,19,23", "tables_0|input_opts|linefilters_0|filter|filter_type": "select_columns", "tables_0|tbl_opts|table_name": "PSMs", "tables_0|tbl_opts|column_names_from_first_line": true, "tables_0|tbl_opts|col_names": "scan,,,,,,confidence", "modify_database|sql_stmts_0|sqlstmt": "UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0", "sqlquery": "SELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")", "query_result|header_prefix": "35", "query_result|header": "yes", "addqueries|queries_0|sqlquery": "SELECT * FROM psms WHERE confidence > 97.0", "addqueries|queries_0|query_result|header_prefix": "", "addqueries|queries_0|query_result|header": "yes"}, "job": {"model_class": "Job", "id": "b057a88c773d1a83", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:05:15.753817", "create_time": "2023-10-26T13:03:11.621847", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "c71426eac153eb4f", "external_id": "gxy-84s9l", "command_line": "cat '/galaxy/server/database/jobs_directory/000/22/configs/tmpysgvmtxa' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/22/configs/tmpk6a5n24g' -Q '/galaxy/server/database/jobs_directory/000/22/configs/tmpysgvmtxa' --comment_char='#' -o '/galaxy/server/database/objects/a/f/a/dataset_afa51f25-1182-4ed2-a39d-25f10b547056.dat'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "addqueries": "{\"queries\": [{\"__index__\": 0, \"query_result\": {\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}, \"sqlquery\": \"SELECT * FROM psms WHERE confidence > 97.0\"}]}", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"35\"}", "sqlquery": "\"SELECT scan,\\\"m/z\\\", \\\"Precursor m/z Error [ppm]\\\", Sequence, \\\"Protein(s)\\\", confidence FROM PSMs WHERE NOT re_search(', ',\\\"Protein(s)\\\")\"", "save_db": "\"false\"", "modify_database": "{\"sql_stmts\": [{\"__index__\": 0, \"sqlstmt\": \"UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0\"}]}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 9, \"columns\": \"1,3,2,6,14,19,23\", \"filter_type\": \"select_columns\"}}]}, \"table\": {\"values\": [{\"id\": 21, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"scan,,,,,,confidence\", \"column_names_from_first_line\": \"true\", \"indexes\": [], \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"table_name\": \"PSMs\"}}]", "add_to_database": "{\"withdb\": null}", "workdb": "\"workdb.sqlite\""}, "inputs": {"tables_0|table": {"id": "bb1a0f380904e977", "src": "hda", "uuid": "10156857-577a-48cd-9667-6b0d6580e9fc"}}, "outputs": {"output": {"id": "b057a88c773d1a83", "src": "hda", "uuid": "afa51f25-1182-4ed2-a39d-25f10b547056"}, "output1": {"id": "4b3533a3fc026109", "src": "hda", "uuid": "df85a916-4e9b-49a0-837b-86c0012286c7"}}, "output_collections": {}, "tool_stdout": "\nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n ", "tool_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/1/0/1/dataset_10156857-577a-48cd-9667-6b0d6580e9fc.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'scan,,,,,,confidence', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19, 23]}]}], 'sql_stmts': ['UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0'], 'queries': [{'query': 'SELECT * FROM psms WHERE confidence > 97.0', 'result_file': 'results0.tsv', 'header': ''}]}\n\nDB modification: UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0 \nrowcount: \n\nSQL: SELECT * FROM psms WHERE confidence > 97.0 \nrowcount: None\n\nSQL: \nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n \nrowcount: None\n", "job_stdout": "", "job_stderr": "", "stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/1/0/1/dataset_10156857-577a-48cd-9667-6b0d6580e9fc.dat', 'table_name': 'PSMs', 'firstlinenames': True, 'column_names': 'scan,,,,,,confidence', 'filters': [{'filter': 'select_columns', 'columns': [1, 3, 2, 6, 14, 19, 23]}]}], 'sql_stmts': ['UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0'], 'queries': [{'query': 'SELECT * FROM psms WHERE confidence > 97.0', 'result_file': 'results0.tsv', 'header': ''}]}\n\nDB modification: UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0 \nrowcount: \n\nSQL: SELECT * FROM psms WHERE confidence > 97.0 \nrowcount: None\n\nSQL: \nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\n \nrowcount: None\n", "stdout": "\nSELECT scan,\"m/z\", \"Precursor m/z Error [ppm]\", Sequence, \"Protein(s)\", confidence FROM PSMs WHERE NOT re_search(', ',\"Protein(s)\")\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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:05:05", "plugin": "core", "name": "start_epoch", "raw_value": "1698325505.0000000"}, {"title": "Job End Time", "value": "2023-10-26 13:05:05", "plugin": "core", "name": "end_epoch", "raw_value": "1698325505.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "query_tabular/3.3.0-9", "has_data": true, "data": {"tool_id": "query_tabular", "tool_version": "3.3.0", "test_index": 9, "time_seconds": 131.12751817703247, "inputs": {"tables_0|table": {"src": "hda", "id": "21d28010d72975c1"}, "tables_0|input_opts|linefilters_0|filter|regex_pattern": "peptide", "tables_0|input_opts|linefilters_0|filter|regex_action": "include_find", "tables_0|input_opts|linefilters_0|filter|filter_type": "regex", "tables_0|tbl_opts|table_name": "epitope", "tables_0|tbl_opts|column_names_from_first_line": true, "sqlquery": "SELECT * FROM epitope", "query_result|header_prefix": "", "query_result|header": "yes"}, "job": {"model_class": "Job", "id": "21d28010d72975c1", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:07:27.082399", "create_time": "2023-10-26T13:05:27.434623", "galaxy_version": "21.09", "command_version": "", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "history_id": "c71426eac153eb4f", "external_id": "gxy-6x9g2", "command_line": "cat '/galaxy/server/database/jobs_directory/000/24/configs/tmpdxd33lf1' && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/cf34c344508d/query_tabular/query_tabular.py' -d -s 'workdb.sqlite' -j '/galaxy/server/database/jobs_directory/000/24/configs/tmp_xu41xfg' -Q '/galaxy/server/database/jobs_directory/000/24/configs/tmpdxd33lf1' -o '/galaxy/server/database/objects/4/f/5/dataset_4f5ed631-f40a-442f-bbb9-10553b60821a.dat'", "traceback": null, "params": {"workdb": "\"workdb.sqlite\"", "add_to_database": "{\"withdb\": null}", "tables": "[{\"__index__\": 0, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"__current_case__\": 8, \"filter_type\": \"regex\", \"regex_action\": \"include_find\", \"regex_pattern\": \"peptide\"}}]}, \"table\": {\"values\": [{\"id\": 24, \"src\": \"hda\"}]}, \"tbl_opts\": {\"col_names\": \"\", \"column_names_from_first_line\": \"true\", \"indexes\": [], \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"table_name\": \"epitope\"}}]", "modify_database": "{\"sql_stmts\": []}", "save_db": "\"false\"", "sqlquery": "\"SELECT * FROM epitope\"", "query_result": "{\"__current_case__\": 0, \"header\": \"yes\", \"header_prefix\": \"\"}", "addqueries": "{\"queries\": []}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"tabular\""}, "inputs": {"tables_0|table": {"id": "21d28010d72975c1", "src": "hda", "uuid": "16355473-ff4d-4ca1-b7f7-6760183f520d"}}, "outputs": {"output": {"id": "ff181ee94a7b5c16", "src": "hda", "uuid": "4f5ed631-f40a-442f-bbb9-10553b60821a"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "\nSELECT * FROM epitope\n ", "job_stderr": "JSON: {'tables': [{'file_path': '/galaxy/server/database/objects/1/6/3/dataset_16355473-ff4d-4ca1-b7f7-6760183f520d.dat', 'table_name': 'epitope', 'firstlinenames': True, 'column_names': '', 'filters': [{'filter': 'regex', 'pattern': 'peptide', 'action': 'include_find'}]}]}\n\nSQL: \nSELECT * FROM epitope\n \nrowcount: None\n", "stderr": "\nJSON: {'tables': [{'file_path': '/galaxy/server/database/objects/1/6/3/dataset_16355473-ff4d-4ca1-b7f7-6760183f520d.dat', 'table_name': 'epitope', 'firstlinenames': True, 'column_names': '', 'filters': [{'filter': 'regex', 'pattern': 'peptide', 'action': 'include_find'}]}]}\n\nSQL: \nSELECT * FROM epitope\n \nrowcount: None\n", "stdout": "\n\nSELECT * FROM epitope\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": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:07:16", "plugin": "core", "name": "start_epoch", "raw_value": "1698325636.0000000"}, {"title": "Job End Time", "value": "2023-10-26 13:07:16", "plugin": "core", "name": "end_epoch", "raw_value": "1698325636.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "samtools_mpileup/2.1.4-0", "has_data": true, "data": {"tool_id": "samtools_mpileup", "tool_version": "2.1.4", "test_index": 0, "time_seconds": 201.98914337158203, "inputs": {"reference_source|input_bam": [{"src": "hda", "id": "147884a71fa4b382"}, {"src": "hda", "id": "274a92894d8d1f5a"}, {"src": "hda", "id": "6c590c910aaa0d77"}], "reference_source|ref_file": {"src": "hda", "id": "f96dd9937b5b7d05"}, "reference_source|reference_source_selector": "history", "advanced_options|limit_by_region|region_paste": "17:100-150", "advanced_options|limit_by_region|limit_by_regions": "limit", "advanced_options|advanced_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "ae1396693019fa0a", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:51:50.058692", "create_time": "2023-10-26T13:48:49.961341", "galaxy_version": "21.09", "command_version": "Version: 1.9 (using htslib 1.9)", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4", "history_id": "c71426eac153eb4f", "external_id": "gxy-wwrdm", "command_line": "ln -s '/galaxy/server/database/objects/7/d/9/dataset_7d9bc0d6-444f-4a68-9321-2490285a04e8.dat' '0' && ln -s '/galaxy/server/database/objects/_metadata_files/f/8/b/metadata_f8b21832-a037-4737-97ee-07287e412268.dat' '0.bai' && ln -s '/galaxy/server/database/objects/b/3/a/dataset_b3a480d1-9e6d-4ca6-87a7-79f7c3f4da52.dat' '1' && ln -s '/galaxy/server/database/objects/_metadata_files/e/9/d/metadata_e9dacef9-426d-42de-aadd-6aa86b253c02.dat' '1.bai' && ln -s '/galaxy/server/database/objects/1/2/1/dataset_1212bbb0-8364-4b6b-b9f2-615c5e577b59.dat' '2' && ln -s '/galaxy/server/database/objects/_metadata_files/3/1/c/metadata_31cc889a-4c9a-44ef-b2d0-be26b5556c89.dat' '2.bai' && ln -s '/galaxy/server/database/objects/4/6/d/dataset_46d54414-7710-408c-8edd-e8d018e68037.dat' && samtools faidx `basename '/galaxy/server/database/objects/4/6/d/dataset_46d54414-7710-408c-8edd-e8d018e68037.dat'` && samtools mpileup -f '/galaxy/server/database/objects/4/6/d/dataset_46d54414-7710-408c-8edd-e8d018e68037.dat' '0' '1' '2' -r '17:100-150' -C 0 -d 8000 -q 0 -Q 13 --output '/galaxy/server/database/objects/4/2/4/dataset_424941e9-b362-4fcb-bbd1-e71c417a2c46.dat'", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_options_cond": "{\"__current_case__\": 0, \"output_options_selector\": \"default\"}", "advanced_options": "{\"__current_case__\": 1, \"advanced_options_selector\": \"advanced\", \"coefficient_for_downgrading\": \"0\", \"disable_probabilistic_realignment\": \"false\", \"exclude_read_group\": {\"__current_case__\": 2, \"exclude_read_groups\": \"no_limit\"}, \"extended_BAQ_computation\": \"false\", \"filter_by_flags\": {\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}, \"ignore_overlaps\": \"false\", \"limit_by_region\": {\"__current_case__\": 0, \"bed_regions\": null, \"limit_by_regions\": \"limit\", \"region_paste\": \"17:100-150\"}, \"max_reads_per_bam\": \"8000\", \"minimum_base_quality\": \"13\", \"minimum_mapping_quality\": \"0\", \"qualities_illumina_onethree\": \"false\", \"skip_anomalous_read_pairs\": \"false\"}", "reference_source": "{\"__current_case__\": 1, \"input_bam\": {\"values\": [{\"id\": 200, \"src\": \"hda\"}, {\"id\": 201, \"src\": \"hda\"}, {\"id\": 202, \"src\": \"hda\"}]}, \"ref_file\": {\"values\": [{\"id\": 203, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_bam1": {"id": "147884a71fa4b382", "src": "hda", "uuid": "7d9bc0d6-444f-4a68-9321-2490285a04e8"}, "input_bam": {"id": "147884a71fa4b382", "src": "hda", "uuid": "7d9bc0d6-444f-4a68-9321-2490285a04e8"}, "input_bam2": {"id": "274a92894d8d1f5a", "src": "hda", "uuid": "b3a480d1-9e6d-4ca6-87a7-79f7c3f4da52"}, "input_bam3": {"id": "6c590c910aaa0d77", "src": "hda", "uuid": "1212bbb0-8364-4b6b-b9f2-615c5e577b59"}, "ref_file": {"id": "f96dd9937b5b7d05", "src": "hda", "uuid": "46d54414-7710-408c-8edd-e8d018e68037"}}, "outputs": {"output_file_pu": {"id": "a00990d46bd1b90e", "src": "hda", "uuid": "424941e9-b362-4fcb-bbd1-e71c417a2c46"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "[mpileup] 3 samples in 3 input files\n", "stderr": "\n[mpileup] 3 samples in 3 input files\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": "2023-10-26 13:51:40", "plugin": "core", "name": "end_epoch", "raw_value": "1698328300.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:51:40", "plugin": "core", "name": "start_epoch", "raw_value": "1698328300.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_mpileup/2.1.4-1", "has_data": true, "data": {"tool_id": "samtools_mpileup", "tool_version": "2.1.4", "test_index": 1, "time_seconds": 140.0020341873169, "inputs": {"reference_source|input_bam": {"src": "hda", "id": "6e7c4599ded8abc5"}, "reference_source|ref_file": {"src": "hda", "id": "376feaacbfca5c54"}, "reference_source|reference_source_selector": "history", "advanced_options|filter_by_flags|exclude_flags": ["4", "16"], "advanced_options|filter_by_flags|filter_flags": "filter", "advanced_options|limit_by_region|region_paste": "17:1050-1060", "advanced_options|limit_by_region|limit_by_regions": "limit", "advanced_options|disable_probabilistic_realignment": true, "advanced_options|advanced_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "4e1e655f8f24586d", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:54:10.425939", "create_time": "2023-10-26T13:52:01.904178", "galaxy_version": "21.09", "command_version": "Version: 1.9 (using htslib 1.9)", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4", "history_id": "c71426eac153eb4f", "external_id": "gxy-b56hw", "command_line": "ln -s '/galaxy/server/database/objects/2/f/f/dataset_2ff08343-4947-4a8b-96e6-2b948569d8a1.dat' '0' && ln -s '/galaxy/server/database/objects/_metadata_files/7/7/b/metadata_77b09760-ab8b-4d27-a8ae-3b165e8658f7.dat' '0.bai' && ln -s '/galaxy/server/database/objects/3/e/4/dataset_3e41430c-d841-43f2-b4e6-d93b27498c0b.dat' && samtools faidx `basename '/galaxy/server/database/objects/3/e/4/dataset_3e41430c-d841-43f2-b4e6-d93b27498c0b.dat'` && samtools mpileup -f '/galaxy/server/database/objects/3/e/4/dataset_3e41430c-d841-43f2-b4e6-d93b27498c0b.dat' '0' --ff 20 -r '17:1050-1060' -B -C 0 -d 8000 -q 0 -Q 13 --output '/galaxy/server/database/objects/9/a/2/dataset_9a25755e-9ab0-48ce-b278-366a0c9794a1.dat'", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_options_cond": "{\"__current_case__\": 0, \"output_options_selector\": \"default\"}", "advanced_options": "{\"__current_case__\": 1, \"advanced_options_selector\": \"advanced\", \"coefficient_for_downgrading\": \"0\", \"disable_probabilistic_realignment\": \"true\", \"exclude_read_group\": {\"__current_case__\": 2, \"exclude_read_groups\": \"no_limit\"}, \"extended_BAQ_computation\": \"false\", \"filter_by_flags\": {\"__current_case__\": 0, \"exclude_flags\": [\"4\", \"16\"], \"filter_flags\": \"filter\", \"require_flags\": null}, \"ignore_overlaps\": \"false\", \"limit_by_region\": {\"__current_case__\": 0, \"bed_regions\": null, \"limit_by_regions\": \"limit\", \"region_paste\": \"17:1050-1060\"}, \"max_reads_per_bam\": \"8000\", \"minimum_base_quality\": \"13\", \"minimum_mapping_quality\": \"0\", \"qualities_illumina_onethree\": \"false\", \"skip_anomalous_read_pairs\": \"false\"}", "reference_source": "{\"__current_case__\": 1, \"input_bam\": {\"values\": [{\"id\": 205, \"src\": \"hda\"}]}, \"ref_file\": {\"values\": [{\"id\": 206, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_bam": {"id": "6e7c4599ded8abc5", "src": "hda", "uuid": "2ff08343-4947-4a8b-96e6-2b948569d8a1"}, "ref_file": {"id": "376feaacbfca5c54", "src": "hda", "uuid": "3e41430c-d841-43f2-b4e6-d93b27498c0b"}}, "outputs": {"output_file_pu": {"id": "725bf0cf4c70645e", "src": "hda", "uuid": "9a25755e-9ab0-48ce-b278-366a0c9794a1"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "[mpileup] 1 samples in 1 input files\n", "stderr": "\n[mpileup] 1 samples in 1 input files\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": "2023-10-26 13:54:01", "plugin": "core", "name": "end_epoch", "raw_value": "1698328441.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:54:01", "plugin": "core", "name": "start_epoch", "raw_value": "1698328441.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_mpileup/2.1.4-2", "has_data": true, "data": {"tool_id": "samtools_mpileup", "tool_version": "2.1.4", "test_index": 2, "time_seconds": 135.53368377685547, "inputs": {"reference_source|input_bam": {"src": "hda", "id": "5a9a3b60115b6288"}, "reference_source|ref_file": {"src": "hda", "id": "fe81b9c7ea22b4a4"}, "reference_source|reference_source_selector": "history", "advanced_options|advanced_options_selector": "default", "output_options_cond|base_position_on_reads": true, "output_options_cond|output_mapping_quality": true, "output_options_cond|output_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "f422c15e29477b69", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:56:25.804170", "create_time": "2023-10-26T13:54:21.790442", "galaxy_version": "21.09", "command_version": "Version: 1.9 (using htslib 1.9)", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4", "history_id": "c71426eac153eb4f", "external_id": "gxy-c4mtf", "command_line": "ln -s '/galaxy/server/database/objects/a/c/1/dataset_ac1abfd4-610c-4726-b746-1f00901d3d7d.dat' '0' && ln -s '/galaxy/server/database/objects/_metadata_files/f/9/8/metadata_f98cf2f0-31a1-4a60-8525-1ad6f62b3a17.dat' '0.bai' && ln -s '/galaxy/server/database/objects/c/e/7/dataset_ce7e6849-aca9-451d-8cfd-662058759dba.dat' && samtools faidx `basename '/galaxy/server/database/objects/c/e/7/dataset_ce7e6849-aca9-451d-8cfd-662058759dba.dat'` && samtools mpileup -f '/galaxy/server/database/objects/c/e/7/dataset_ce7e6849-aca9-451d-8cfd-662058759dba.dat' '0' -O -s --output '/galaxy/server/database/objects/1/3/f/dataset_13f955b8-7fd2-4d3f-a8d3-2e165116c523.dat'", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_options_cond": "{\"__current_case__\": 1, \"base_position_on_reads\": \"true\", \"output_all_pos\": \"\", \"output_mapping_quality\": \"true\", \"output_options_selector\": \"advanced\", \"output_read_names\": \"false\"}", "advanced_options": "{\"__current_case__\": 0, \"advanced_options_selector\": \"default\"}", "reference_source": "{\"__current_case__\": 1, \"input_bam\": {\"values\": [{\"id\": 208, \"src\": \"hda\"}]}, \"ref_file\": {\"values\": [{\"id\": 209, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_bam": {"id": "5a9a3b60115b6288", "src": "hda", "uuid": "ac1abfd4-610c-4726-b746-1f00901d3d7d"}, "ref_file": {"id": "fe81b9c7ea22b4a4", "src": "hda", "uuid": "ce7e6849-aca9-451d-8cfd-662058759dba"}}, "outputs": {"output_file_pu": {"id": "341c621b10b35f83", "src": "hda", "uuid": "13f955b8-7fd2-4d3f-a8d3-2e165116c523"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "[mpileup] 1 samples in 1 input files\n", "stderr": "\n[mpileup] 1 samples in 1 input files\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": "2023-10-26 13:56:16", "plugin": "core", "name": "end_epoch", "raw_value": "1698328576.0000000"}, {"title": "Job Start Time", "value": "2023-10-26 13:56:15", "plugin": "core", "name": "start_epoch", "raw_value": "1698328575.0000000"}, {"title": "Memory Allocated (MB)", "value": "2000", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "2000.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_mpileup/2.1.4-3", "has_data": true, "data": {"tool_id": "samtools_mpileup", "tool_version": "2.1.4", "test_index": 3, "time_seconds": 133.43437314033508, "inputs": {"reference_source|input_bam": {"src": "hda", "id": "c4b5f6b3b537a958"}, "reference_source|ref_file": {"src": "hda", "id": "65ec03c56f9c20f7"}, "reference_source|reference_source_selector": "history", "advanced_options|skip_anomalous_read_pairs": true, "advanced_options|advanced_options_selector": "advanced", "output_options_cond|output_options_selector": "default"}, "job": {"model_class": "Job", "id": "931816e04032d6bf", "state": "ok", "exit_code": 0, "update_time": "2023-10-26T13:58:39.250919", "create_time": "2023-10-26T13:56:37.281628", "galaxy_version": "21.09", "command_version": "Version: 1.9 (using htslib 1.9)", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4", "history_id": "c71426eac153eb4f", "external_id": "gxy-n4jfv", "command_line": "ln -s '/galaxy/server/database/objects/b/9/3/dataset_b9321d1e-b2e6-4f4b-a4c9-946ecce8e92f.dat' '0' && ln -s '/galaxy/server/database/objects/_metadata_files/d/3/3/metadata_d33ea570-14de-417c-9459-f78a4c7fb24e.dat' '0.bai' && ln -s '/galaxy/server/database/objects/0/1/e/dataset_01e8d5cd-41c2-41f0-bf2b-c9bfdbef9c43.dat' && samtools faidx `basename '/galaxy/server/database/objects/0/1/e/dataset_01e8d5cd-41c2-41f0-bf2b-c9bfdbef9c43.dat'` && samtools mpileup -f '/galaxy/server/database/objects/0/1/e/dataset_01e8d5cd-41c2-41f0-bf2b-c9bfdbef9c43.dat' '0' -A -C 0 -d 8000 -q 0 -Q 13 --output '/galaxy/server/database/objects/f/3/5/dataset_f352b3f1-b953-4662-9d10-cdd3bc9de78e.dat'", "traceback": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_options_cond": "{\"__current_case__\": 0, \"output_options_selector\": \"default\"}", "advanced_options": "{\"__current_case__\": 1, \"advanced_options_selector\": \"advanced\", \"coefficient_for_downgrading\": \"0\", \"disable_probabilistic_realignment\": \"false\", \"exclude_read_group\": {\"__current_case__\": 2, \"exclude_read_groups\": \"no_limit\"}, \"extended_BAQ_computation\": \"false\", \"filter_by_flags\": {\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}, \"ignore_overlaps\": \"false\", 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