From 65fde16c48afc05804684006e0e6b5e3342bae28 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Wed, 25 Sep 2024 19:48:45 +0000 Subject: [PATCH] Updating anvil-edge README for edge-24-09-25-18-17-1 --- reports/anvil-edge/README.md | 2 +- reports/anvil-edge/tool-tests/chunks.json | 10 +- .../edge-24-09-25-18-17-1/chunk.json | 7 + .../edge-24-09-25-18-17-1/chunk.txt | 25 + .../errors/10b588686dd359bf.json | 45 + .../errors/10c52727a6cf2bc6.json | 59 + .../errors/120c2a079f3eac9d.json | 45 + .../errors/198305c58f4c58c0.json | 60 + .../errors/24f4a942c09aed0a.json | 45 + .../errors/271fdef17e8ec9e0.json | 52 + .../errors/322b41b111112430.json | 45 + .../errors/485eb734f0ba54cf.json | 58 + .../errors/5799f3c77c3f3473.json | 45 + .../errors/8883cf3d719ee65e.json | 45 + .../errors/8a8d7a47f4b0f907.json | 45 + .../errors/8b79a822eb52182f.json | 45 + .../errors/c4161aec13e7ea95.json | 45 + .../errors/c46d92a1e6cf00ac.json | 45 + .../errors/c6b7396d5a2f6aa3.json | 48 + .../errors/d6423205e7e49dd3.json | 45 + .../errors/f6e2a75ac3682018.json | 45 + .../edge-24-09-25-18-17-1/job-metrics.csv | 223 ++++ .../tool-tests/edge-24-09-25-18-17-1/jobs.txt | 222 ++++ .../edge-24-09-25-18-17-1/results.html | 291 +++++ .../edge-24-09-25-18-17-1/results.json | 1 + .../edge-24-09-25-18-17-1/results.xunit | 1068 +++++++++++++++++ .../edge-24-09-25-18-17-1/tools.yml | 127 ++ 27 files changed, 2787 insertions(+), 6 deletions(-) create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/chunk.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/chunk.txt create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/10b588686dd359bf.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/10c52727a6cf2bc6.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/120c2a079f3eac9d.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/198305c58f4c58c0.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/24f4a942c09aed0a.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/271fdef17e8ec9e0.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/322b41b111112430.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/485eb734f0ba54cf.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/5799f3c77c3f3473.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/8883cf3d719ee65e.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/8a8d7a47f4b0f907.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/8b79a822eb52182f.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/c4161aec13e7ea95.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/c46d92a1e6cf00ac.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/c6b7396d5a2f6aa3.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/d6423205e7e49dd3.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/f6e2a75ac3682018.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/job-metrics.csv create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/jobs.txt create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/results.html create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/results.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/results.xunit create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/tools.yml diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md index 5cc239edb..8f79b7f76 100644 --- a/reports/anvil-edge/README.md +++ b/reports/anvil-edge/README.md @@ -13,4 +13,4 @@ After each successful deployment, automated tool tests are also run against the Latest tool tests for each chunk: -
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 23 06:26:44 2024Mon Sep 16 06:27:02 2024
1ToolsetMon Sep 23 18:33:07 2024Mon Sep 16 18:32:01 2024
2ToolsetTue Sep 24 06:26:56 2024Tue Sep 17 06:26:34 2024
3ToolsetTue Sep 24 18:32:18 2024Tue Sep 17 18:34:01 2024
4ToolsetWed Sep 25 06:26:23 2024Wed Sep 18 06:26:06 2024
5ToolsetWed Sep 18 18:32:06 2024Wed Sep 11 18:32:01 2024
6ToolsetThu Sep 19 06:26:39 2024Thu Sep 12 06:26:50 2024
7ToolsetThu Sep 19 18:31:09 2024Thu Sep 12 18:33:11 2024
8ToolsetFri Sep 20 06:25:56 2024Fri Sep 13 06:26:17 2024
9ToolsetFri Sep 20 18:32:50 2024Fri Sep 13 18:32:19 2024
10ToolsetSat Sep 21 06:25:16 2024Sat Sep 14 06:24:56 2024
11ToolsetSat Sep 21 18:31:38 2024Sat Sep 14 18:30:22 2024
12ToolsetSun Sep 22 06:25:20 2024Sun Sep 15 06:25:35 2024
13ToolsetSun Sep 22 18:31:24 2024Sun Sep 15 18:32:12 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 23 06:26:44 2024Mon Sep 16 06:27:02 2024
1ToolsetMon Sep 23 18:33:07 2024Mon Sep 16 18:32:01 2024
2ToolsetTue Sep 24 06:26:56 2024Tue Sep 17 06:26:34 2024
3ToolsetTue Sep 24 18:32:18 2024Tue Sep 17 18:34:01 2024
4ToolsetWed Sep 25 06:26:23 2024Wed Sep 18 06:26:06 2024
5ToolsetWed Sep 25 18:31:33 2024Wed Sep 18 18:32:06 2024
6ToolsetThu Sep 19 06:26:39 2024Thu Sep 12 06:26:50 2024
7ToolsetThu Sep 19 18:31:09 2024Thu Sep 12 18:33:11 2024
8ToolsetFri Sep 20 06:25:56 2024Fri Sep 13 06:26:17 2024
9ToolsetFri Sep 20 18:32:50 2024Fri Sep 13 18:32:19 2024
10ToolsetSat Sep 21 06:25:16 2024Sat Sep 14 06:24:56 2024
11ToolsetSat Sep 21 18:31:38 2024Sat Sep 14 18:30:22 2024
12ToolsetSun Sep 22 06:25:20 2024Sun Sep 15 06:25:35 2024
13ToolsetSun Sep 22 18:31:24 2024Sun Sep 15 18:32:12 2024
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json index f80225dd2..a5401dca0 100644 --- a/reports/anvil-edge/tool-tests/chunks.json +++ b/reports/anvil-edge/tool-tests/chunks.json @@ -28,11 +28,11 @@ "date2": "Wed Sep 18 06:26:06 2024" }, "5": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-18-18-17-1/results.html", - "date1": "Wed Sep 18 18:32:06 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-18-18-17-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-11-18-16-1/results.html", - "date2": "Wed Sep 11 18:32:01 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/results.html", + "date1": "Wed Sep 25 18:31:33 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-18-18-17-1/results.html", + "date2": "Wed Sep 18 18:32:06 2024" }, "6": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-19-06-11-1/results.html", diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/chunk.json new file mode 100644 index 000000000..bbef00395 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/chunk.json @@ -0,0 +1,7 @@ +{ + "5": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/results.html", + "date1": "Wed Sep 25 18:31:33 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/chunk.txt new file mode 100644 index 000000000..b50e02586 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/chunk.txt @@ -0,0 +1,25 @@ +-t collapse_collections --tool-version 90981f86000f +-t deeptools_multi_bam_summary --tool-version 78f405266706 +-t fastq_paired_end_deinterlacer --tool-version f3936d0632cb +-t circos --tool-version df7356989ac1 +-t mummer_mummer --tool-version 48823c9635a4 +-t porechop --tool-version 93d623d9979c +-t limma_voom --tool-version 0921444c832d +-t limma_voom --tool-version d6f5fa4ee473 +-t sam2interval --tool-version 75557c0908a9 +-t samtools_flagstat --tool-version 22970df7a40e +-t music_construct_eset --tool-version 282819d09a4f +-t music_construct_eset --tool-version 2cfd0db49bbc +-t raceid_clustering --tool-version a4b734cd253b +-t raceid_clustering --tool-version f911a64454fb +-t scanpy_filter --tool-version b409c2486353 +-t scanpy_normalise_data --tool-version 439f7f939d46 +-t scanpy_normalise_data --tool-version 463d4fa8f5ec +-t annotatemyids --tool-version 44018dd6b447 +-t annotatemyids --tool-version fe3ca740a485 +-t diff --tool-version 156d0908e232 +-t bcftools_consensus --tool-version d6dc477167f8 +-t bcftools_plugin_impute_info --tool-version 776ad0b21536 +-t bcftools_query --tool-version c9c5718edc19 +-t vcfgeno2haplo --tool-version a3dea556218d +-t ivar_trim --tool-version db536ad45f28 diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/10b588686dd359bf.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/10b588686dd359bf.json new file mode 100644 index 000000000..664d60113 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/10b588686dd359bf.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "10b588686dd359bf", + "history_id": "beda644706419afa", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T19:10:42.331401", + "update_time": "2024-09-25T19:10:54.520011", + "galaxy_version": "24.1", + "external_id": "gxy-hpb4l", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/127/registry.xml' '/galaxy/server/database/jobs_directory/000/127/upload_params.json' '175:/galaxy/server/database/objects/b/9/e/dataset_b9e096b6-8cd6-4939-a92c-f6446b2a3946_files:/galaxy/server/database/objects/b/9/e/dataset_b9e096b6-8cd6-4939-a92c-f6446b2a3946.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_nl21f4zp\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"matrix.filter.rdat\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_b2zy23wu\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "83cfe499f71f57ee", + "src": "hda", + "uuid": "b9e096b6-8cd6-4939-a92c-f6446b2a3946" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/10c52727a6cf2bc6.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/10c52727a6cf2bc6.json new file mode 100644 index 000000000..fafb13ba1 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/10c52727a6cf2bc6.json @@ -0,0 +1,59 @@ +{ + "model_class": "Job", + "id": "10c52727a6cf2bc6", + "history_id": "beda644706419afa", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T19:38:19.713458", + "update_time": "2024-09-25T19:38:25.306243", + "galaxy_version": "24.1", + "external_id": "gxy-r4r55", + "handler": null, + "job_runner_name": null, + "command_line": "diff -u '/galaxy/server/database/objects/9/4/8/dataset_94818178-a034-419c-b3e2-d7f0fafb1861.dat' '/galaxy/server/database/objects/9/4/8/dataset_94818178-a034-419c-b3e2-d7f0fafb1861.dat' > '/galaxy/server/database/objects/9/8/9/dataset_98993230-2033-44e0-a793-95e7771ffbb8.dat'; sed -e 's/@@title@@/Diff report for \"file 3.txt\" and \"file 3.txt\"/g' -e 's/@@outputformat@@/'side-by-side'/g' -e '/@@diffoutput@@/{r'/galaxy/server/database/objects/9/8/9/dataset_98993230-2033-44e0-a793-95e7771ffbb8.dat'' -e ';d}' '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/diff/156d0908e232/diff/template.html' > '/galaxy/server/database/objects/3/2/c/dataset_32c26dc8-bc80-4d21-a614-54f50496d495.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"txt\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "output_format": "\"side-by-side\"", + "generate_report": "true" + }, + "inputs": { + "input1": { + "id": "225d5899908dbd3e", + "src": "hda", + "uuid": "94818178-a034-419c-b3e2-d7f0fafb1861" + }, + "input2": { + "id": "225d5899908dbd3e", + "src": "hda", + "uuid": "94818178-a034-419c-b3e2-d7f0fafb1861" + } + }, + "outputs": { + "diff_file": { + "id": "24eb12e4dc7da3c5", + "src": "hda", + "uuid": "98993230-2033-44e0-a793-95e7771ffbb8" + }, + "html_file": { + "id": "735adcc660abafa2", + "src": "hda", + "uuid": "32c26dc8-bc80-4d21-a614-54f50496d495" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/120c2a079f3eac9d.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/120c2a079f3eac9d.json new file mode 100644 index 000000000..1111cc1a2 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/120c2a079f3eac9d.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "120c2a079f3eac9d", + "history_id": "beda644706419afa", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T18:37:39.945190", + "update_time": "2024-09-25T18:37:53.614364", + "galaxy_version": "24.1", + "external_id": "gxy-6zmgg", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/15/registry.xml' '/galaxy/server/database/jobs_directory/000/15/upload_params.json' '26:/galaxy/server/database/objects/c/a/1/dataset_ca148397-4d7e-4291-a0ff-7c05d56a8017_files:/galaxy/server/database/objects/c/a/1/dataset_ca148397-4d7e-4291-a0ff-7c05d56a8017.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_yzqobvwo\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"input.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_xfrjk0pm\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "271fdef17e8ec9e0", + "src": "hda", + "uuid": "ca148397-4d7e-4291-a0ff-7c05d56a8017" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/198305c58f4c58c0.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/198305c58f4c58c0.json new file mode 100644 index 000000000..b4ad54a53 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/198305c58f4c58c0.json @@ -0,0 +1,60 @@ +{ + "model_class": "Job", + "id": "198305c58f4c58c0", + "history_id": "beda644706419afa", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T19:07:23.569551", + "update_time": "2024-09-25T19:07:32.815242", + "galaxy_version": "24.1", + "external_id": "gxy-7qr44", + "handler": null, + "job_runner_name": null, + "command_line": "Rscript --vanilla '/galaxy/server/database/jobs_directory/000/122/configs/tmpe2ov9io4'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "expdata": "{\"abstract\": \"An example ExpressionSet\", \"contact\": \"pfermat@lab.not.exist\", \"lab\": \"Francis Galton Lab\", \"name\": \"Pierre Fermat\", \"other\": [{\"__index__\": 0, \"comment\": \"Created in Galaxy\", \"field\": \"notes\"}, {\"__index__\": 1, \"comment\": \"Some other comment\", \"field\": \"general\"}], \"title\": \"Smoking-Cancer Experiment\", \"url\": \"www.lab.not.exist\"}", + "metadata": "[{\"__index__\": 0, \"label_desc\": \"Patient gender\", \"row_names\": \"gender\"}, {\"__index__\": 1, \"label_desc\": \"Case/control status\", \"row_names\": \"type\"}, {\"__index__\": 2, \"label_desc\": \"Tumor Progress on XYZ scale\", \"row_names\": \"score\"}]", + "annotation": "\"hgu95av2\"" + }, + "inputs": { + "exprs_file": { + "id": "8970d1187d6ee4e3", + "src": "hda", + "uuid": "8c741297-978b-46e6-912a-31e53d279bf9" + }, + "pdata_file": { + "id": "e69c2b3720943dd4", + "src": "hda", + "uuid": "1aab4e58-8554-481b-acd5-5846b64c1eff" + } + }, + "outputs": { + "out_tab": { + "id": "16f084dc7582ea60", + "src": "hda", + "uuid": "b0d428d0-0bf6-43d9-b7d3-0944d265c156" + }, + "out_rds": { + "id": "826345b6d8739074", + "src": "hda", + "uuid": "9489797a-0139-4dcb-968d-7dcf682b1bb2" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/24f4a942c09aed0a.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/24f4a942c09aed0a.json new file mode 100644 index 000000000..b636b39ed --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/24f4a942c09aed0a.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "24f4a942c09aed0a", + "history_id": "beda644706419afa", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T18:43:28.438343", + "update_time": "2024-09-25T18:43:40.643415", + "galaxy_version": "24.1", + "external_id": "gxy-9pb4d", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/35/registry.xml' '/galaxy/server/database/jobs_directory/000/35/upload_params.json' '48:/galaxy/server/database/objects/2/3/5/dataset_235942e9-02ff-4b64-889f-da59f5fcf00e_files:/galaxy/server/database/objects/2/3/5/dataset_235942e9-02ff-4b64-889f-da59f5fcf00e.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_cek8kais\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"matrix.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_fw41b2ig\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "31c7b452295615c3", + "src": "hda", + "uuid": "235942e9-02ff-4b64-889f-da59f5fcf00e" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/271fdef17e8ec9e0.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/271fdef17e8ec9e0.json new file mode 100644 index 000000000..66b05e7a2 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/271fdef17e8ec9e0.json @@ -0,0 +1,52 @@ +{ + "model_class": "Job", + "id": "271fdef17e8ec9e0", + "history_id": "beda644706419afa", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T18:39:53.021927", + "update_time": "2024-09-25T18:39:57.805896", + "galaxy_version": "24.1", + "external_id": "gxy-z76bg", + "handler": null, + "job_runner_name": null, + "command_line": "porechop -i '/galaxy/server/database/objects/b/e/d/dataset_bed07ad6-cd8a-4669-b60f-4850db752d72.dat' --format 'fastq' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fastq'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", + "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", + "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", + "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", + "format": "\"fastq\"" + }, + "inputs": { + "input_file": { + "id": "e5551c944ebef800", + "src": "hda", + "uuid": 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Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/26/working/out.fastq\n\n", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/b/e/d/dataset_bed07ad6-cd8a-4669-b60f-4850db752d72.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/26/working/out.fastq\n\n", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/322b41b111112430.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/322b41b111112430.json new file mode 100644 index 000000000..f39594025 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/322b41b111112430.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "322b41b111112430", + "history_id": "beda644706419afa", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T19:00:45.364918", + "update_time": "2024-09-25T19:00:59.109973", + "galaxy_version": "24.1", + "external_id": "gxy-fdhhq", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/101/registry.xml' '/galaxy/server/database/jobs_directory/000/101/upload_params.json' '136:/galaxy/server/database/objects/5/e/0/dataset_5e05bf64-51a9-41f6-bf84-f52586742014_files:/galaxy/server/database/objects/5/e/0/dataset_5e05bf64-51a9-41f6-bf84-f52586742014.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_5je1ch7q\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"anno.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_vaw0f4vy\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "0879ef412951d73b", + "src": "hda", + "uuid": "5e05bf64-51a9-41f6-bf84-f52586742014" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/485eb734f0ba54cf.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/485eb734f0ba54cf.json new file mode 100644 index 000000000..5a7790bb8 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/485eb734f0ba54cf.json @@ -0,0 +1,58 @@ +{ + "model_class": "Job", + "id": "485eb734f0ba54cf", + "history_id": "beda644706419afa", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T19:41:05.832557", + "update_time": "2024-09-25T19:41:11.148060", + "galaxy_version": "24.1", + "external_id": "gxy-chmbv", + "handler": null, + "job_runner_name": null, + "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/6/f/b/dataset_6fb4252f-5187-4e87-911a-98c86cb1bee5.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/d/4/4/dataset_d44efd32-fcc4-4a55-9a92-6d6b03bc9836.dat' ref.fa && samtools faidx ref.fa && bcftools consensus --fasta-ref ref.fa --include 'TYPE=\"snp\"' --absent 'W' --output '/galaxy/server/database/objects/d/7/f/dataset_d7fb38a6-075c-42eb-93f3-e351e4456e28.dat' input.vcf.gz", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "sec_restrict": "{\"exclude\": null, \"include\": \"TYPE=\\\"snp\\\"\"}", + "absent": "\"W\"", + "rename": "false", + "chain": "false", + "sec_default": "{\"conditional_mask\": {\"__current_case__\": 0, \"selector\": \"disabled\"}, \"iupac_codes\": false, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"mask\": null, \"sample\": null, \"select_haplotype\": null}", + "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 273, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}" + }, + "inputs": { + "input_file": { + "id": "9d24a7dcc9e55344", + "src": "hda", + "uuid": "6fb4252f-5187-4e87-911a-98c86cb1bee5" + }, + "reference_source|fasta_ref": { + "id": "7a7325487ad2c378", + "src": "hda", + "uuid": "d44efd32-fcc4-4a55-9a92-6d6b03bc9836" + } + }, + "outputs": { + "output_file": { + "id": "d21c8ecbbf22e9c2", + "src": "hda", + "uuid": "d7fb38a6-075c-42eb-93f3-e351e4456e28" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 6 variants\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 6 variants\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/5799f3c77c3f3473.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/5799f3c77c3f3473.json new file mode 100644 index 000000000..de4191437 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/5799f3c77c3f3473.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "5799f3c77c3f3473", + "history_id": "beda644706419afa", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T18:58:14.382520", + "update_time": "2024-09-25T18:58:29.249251", + "galaxy_version": "24.1", + "external_id": "gxy-bzpn5", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/84/registry.xml' '/galaxy/server/database/jobs_directory/000/84/upload_params.json' '118:/galaxy/server/database/objects/8/c/5/dataset_8c549a94-6bc7-4259-994d-94c8a616d948_files:/galaxy/server/database/objects/8/c/5/dataset_8c549a94-6bc7-4259-994d-94c8a616d948.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_ghpsv3nt\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"WT2.counts\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_yta1_ej2\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "95bcae0792b26f01", + "src": "hda", + "uuid": "8c549a94-6bc7-4259-994d-94c8a616d948" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/8883cf3d719ee65e.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/8883cf3d719ee65e.json new file mode 100644 index 000000000..1acb9e877 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/8883cf3d719ee65e.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "8883cf3d719ee65e", + "history_id": "beda644706419afa", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T18:51:53.602154", + "update_time": "2024-09-25T18:52:05.517730", + "galaxy_version": "24.1", + "external_id": "gxy-9qczf", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/67/registry.xml' '/galaxy/server/database/jobs_directory/000/67/upload_params.json' '91:/galaxy/server/database/objects/2/b/4/dataset_2b401597-0a4e-49df-9fbd-ab2d4c949310_files:/galaxy/server/database/objects/2/b/4/dataset_2b401597-0a4e-49df-9fbd-ab2d4c949310.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_rlc700fr\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"matrix.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_x6v7xx0e\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "a3f3d02b24801f07", + "src": "hda", + "uuid": "2b401597-0a4e-49df-9fbd-ab2d4c949310" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/8a8d7a47f4b0f907.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/8a8d7a47f4b0f907.json new file mode 100644 index 000000000..432ab3276 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/8a8d7a47f4b0f907.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "8a8d7a47f4b0f907", + "history_id": "beda644706419afa", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T18:47:47.237905", + "update_time": "2024-09-25T18:48:03.164766", + "galaxy_version": "24.1", + "external_id": "gxy-gd46l", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/47/registry.xml' '/galaxy/server/database/jobs_directory/000/47/upload_params.json' '67:/galaxy/server/database/objects/f/0/7/dataset_f07ae78e-5c2c-46cd-95c9-c921059b2c04_files:/galaxy/server/database/objects/f/0/7/dataset_f07ae78e-5c2c-46cd-95c9-c921059b2c04.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_8sxg13v9\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"WT2.counts\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_dhmyxxhj\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "8883cf3d719ee65e", + "src": "hda", + "uuid": "f07ae78e-5c2c-46cd-95c9-c921059b2c04" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/8b79a822eb52182f.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/8b79a822eb52182f.json new file mode 100644 index 000000000..b4538db3b --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/8b79a822eb52182f.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "8b79a822eb52182f", + "history_id": "beda644706419afa", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T19:35:33.614507", + "update_time": "2024-09-25T19:35:47.684275", + "galaxy_version": "24.1", + "external_id": "gxy-6x9cf", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/171/registry.xml' '/galaxy/server/database/jobs_directory/000/171/upload_params.json' '243:/galaxy/server/database/objects/8/f/d/dataset_8fdcbf65-19a3-45a7-988d-7e86ace35c89_files:/galaxy/server/database/objects/8/f/d/dataset_8fdcbf65-19a3-45a7-988d-7e86ace35c89.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_gfxued7f\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"file1.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_s77srvbq\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "6a6ba1d8a3ebad10", + "src": "hda", + "uuid": "8fdcbf65-19a3-45a7-988d-7e86ace35c89" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/c4161aec13e7ea95.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/c4161aec13e7ea95.json new file mode 100644 index 000000000..6b3531731 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/c4161aec13e7ea95.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "c4161aec13e7ea95", + "history_id": "beda644706419afa", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T18:58:50.747584", + "update_time": "2024-09-25T18:59:40.131519", + "galaxy_version": "24.1", + "external_id": "gxy-j4jnk", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/96/registry.xml' '/galaxy/server/database/jobs_directory/000/96/upload_params.json' '130:/galaxy/server/database/objects/f/c/3/dataset_fc367a08-95b7-46b9-a27b-5ba3ea81e571_files:/galaxy/server/database/objects/f/c/3/dataset_fc367a08-95b7-46b9-a27b-5ba3ea81e571.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_804pmqm3\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"matrix.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_rv6wmoqz\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"auto\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "11d166bced681358", + "src": "hda", + "uuid": "fc367a08-95b7-46b9-a27b-5ba3ea81e571" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/c46d92a1e6cf00ac.json b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/c46d92a1e6cf00ac.json new file mode 100644 index 000000000..3d1cf4ca0 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/c46d92a1e6cf00ac.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "c46d92a1e6cf00ac", + "history_id": "beda644706419afa", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T18:37:54.995527", + "update_time": "2024-09-25T18:38:07.721324", + "galaxy_version": "24.1", + "external_id": "gxy-mfszw", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/19/registry.xml' '/galaxy/server/database/jobs_directory/000/19/upload_params.json' '30:/galaxy/server/database/objects/8/0/7/dataset_80717aaf-d579-4e0b-a777-4b7504a2fbac_files:/galaxy/server/database/objects/8/0/7/dataset_80717aaf-d579-4e0b-a777-4b7504a2fbac.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_p0wd9scw\"", + "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": 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b/reports/anvil-edge/tool-tests/edge-24-09-25-18-17-1/errors/c6b7396d5a2f6aa3.json @@ -0,0 +1,48 @@ +{ + "model_class": "Job", + "id": "c6b7396d5a2f6aa3", + "history_id": "beda644706419afa", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2", + "state": "error", + "exit_code": null, + "create_time": "2024-09-25T19:03:53.758269", + "update_time": "2024-09-25T19:03:58.926686", + "galaxy_version": "24.1", + "external_id": "gxy-wfr6g", + "handler": null, + "job_runner_name": null, + "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/75557c0908a9/sam2interval/sam2interval.py' --input_sam_file='/galaxy/server/database/objects/a/9/3/dataset_a936a266-0383-4436-94d1-4efe6785524c.dat' > '/galaxy/server/database/objects/8/e/9/dataset_8e9b4bf4-62b3-4135-ab39-446888d65808.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + 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"tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:many mapping between keys and columns\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:many mapping between keys and columns\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "25 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "25.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:33:09", "plugin": "core", "name": "end_epoch", "raw_value": "1727292789.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:32:44", "plugin": "core", "name": "start_epoch", "raw_value": "1727292764.0000000"}, {"title": "Memory Allocated (MB)", "value": 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OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:many mapping between keys and columns\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:many mapping between keys and columns\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "24 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "24.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:30:00", "plugin": "core", "name": "end_epoch", "raw_value": "1727292600.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:29:36", "plugin": "core", "name": "start_epoch", "raw_value": "1727292576.0000000"}, {"title": "Memory Allocated (MB)", "value": "8589", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8589.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "annotatemyids/3.5.0.1-3", "has_data": true, "data": {"tool_id": "annotatemyids", "tool_version": "3.5.0.1", "test_index": 3, "time_seconds": 86.25675082206726, "inputs": {"id_file": {"src": "hda", "id": "e6451b95c7e2ce3a"}, "organism": "Hs", "id_type": "ENSEMBL", "output_cols": ["ENSEMBL", "GO", "ONTOLOGY", "EVIDENCE"], "remove_dups": true}, "job": {"model_class": "Job", "id": "194c88fab6466fe2", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:33:44.446207", "update_time": "2024-09-25T19:34:48.304770", "galaxy_version": "24.1", "external_id": "gxy-zvnhx", "handler": null, "job_runner_name": null, "command_line": "Rscript '/galaxy/server/database/jobs_directory/000/168/configs/tmpdr_p1cfz'", "user_email": 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returned 1:many mapping between keys and columns\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:many mapping between keys and columns\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "24 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "24.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:34:35", "plugin": "core", "name": "end_epoch", "raw_value": "1727292875.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:34:11", "plugin": "core", "name": "start_epoch", "raw_value": "1727292851.0000000"}, {"title": "Memory Allocated (MB)", "value": "8589", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8589.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_consensus/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_consensus", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 50.725356340408325, "inputs": {"input_file": {"src": "hda", "id": "dd73bcbd31649b23"}, "reference_source|fasta_ref": {"src": "hda", "id": "1f7fb387917afb12"}, "reference_source|reference_source_selector": "history", "sec_default|mask": {"src": "hda", "id": "09b54d48ea282501"}, "chain": true}, "job": {"model_class": "Job", "id": "cf1f1f5eb7c5879c", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:38:56.012172", "update_time": "2024-09-25T19:39:16.939438", "galaxy_version": "24.1", "external_id": "gxy-tx64g", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/c/b/2/dataset_cb24ecc3-d8c3-4daf-b92a-7c58bf29a8af.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/b/e/7/dataset_be7649cb-d8f9-40d0-86ac-11a7e29c674a.dat' ref.fa && samtools faidx ref.fa && bcftools consensus --fasta-ref ref.fa --mask '/galaxy/server/database/objects/e/a/5/dataset_ea5162d2-c722-47b3-bf2a-8315b0810176.dat' --chain '/galaxy/server/database/objects/5/e/3/dataset_5e3c240f-ad86-4dc7-9e50-343fabfd5808.dat' --output '/galaxy/server/database/objects/4/3/e/dataset_43e14c93-e02e-479e-b35b-ab9a839963d1.dat' input.vcf.gz", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_restrict": "{\"exclude\": null, \"include\": null}", "absent": "\"\"", "rename": "false", "chain": "true", "sec_default": "{\"conditional_mask\": {\"__current_case__\": 0, \"selector\": \"disabled\"}, \"iupac_codes\": false, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"mask\": {\"values\": [{\"id\": 262, \"src\": \"hda\"}]}, \"sample\": null, \"select_haplotype\": null}", "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 261, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_file": {"id": "dd73bcbd31649b23", "src": "hda", "uuid": "cb24ecc3-d8c3-4daf-b92a-7c58bf29a8af"}, "reference_source|fasta_ref": {"id": "1f7fb387917afb12", "src": "hda", "uuid": "be7649cb-d8f9-40d0-86ac-11a7e29c674a"}, "sec_default|mask": {"id": "09b54d48ea282501", "src": "hda", "uuid": "ea5162d2-c722-47b3-bf2a-8315b0810176"}}, "outputs": {"output_file": {"id": "a6085f0e4625b1e8", "src": "hda", "uuid": "43e14c93-e02e-479e-b35b-ab9a839963d1"}, "chain_file": {"id": "789f298ccc65ab24", "src": "hda", "uuid": "5e3c240f-ad86-4dc7-9e50-343fabfd5808"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 12 variants\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 12 variants\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:39:02", "plugin": "core", "name": "end_epoch", "raw_value": "1727293142.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:39:01", "plugin": "core", "name": "start_epoch", "raw_value": "1727293141.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_consensus/1.15.1+galaxy4-1", "has_data": true, "data": {"tool_id": "bcftools_consensus", "tool_version": "1.15.1+galaxy4", "test_index": 1, "status": "skip"}}, {"id": "bcftools_consensus/1.15.1+galaxy4-2", "has_data": true, "data": {"tool_id": "bcftools_consensus", "tool_version": "1.15.1+galaxy4", "test_index": 2, "time_seconds": 44.34570097923279, "inputs": {"input_file": {"src": "hda", "id": "652697a80da4fc96"}, "reference_source|fasta_ref": {"src": "hda", "id": "b4e272fcf3820c05"}, "reference_source|reference_source_selector": "history", "sec_default|mask": {"src": "hda", "id": "f5609ab2bcfa2ba6"}, "chain": false, "rename": true}, "job": {"model_class": "Job", "id": "47200227da8521cf", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:39:47.076792", "update_time": "2024-09-25T19:40:01.594237", "galaxy_version": "24.1", "external_id": "gxy-kzp4z", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/0/a/1/dataset_0a142ea4-6eb4-4686-a39b-061a3411d5ae.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/1/1/7/dataset_11779aa8-a59d-4c23-b5d6-0bc41cd1fbc1.dat' ref.fa && samtools faidx ref.fa && bcftools consensus --fasta-ref ref.fa --mask '/galaxy/server/database/objects/5/3/1/dataset_531c5a98-4a25-479b-9a1a-dd7722717660.dat' input.vcf.gz | awk 'BEGIN {i=1} {if (match($0, /^>/)) {if (i==1) {name=\"consensus.vcf\"} else {name=sprintf(\"%s-%d\",\"consensus.vcf\",i);} print(gensub(/>[^ ]+( ?.*)/, \">\" name \"\\\\1\", 1)); i=i+1;} else {print}}' > '/galaxy/server/database/objects/8/1/4/dataset_814f42c2-903c-4568-b6fd-f72a31e56241.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_restrict": "{\"exclude\": null, \"include\": null}", "absent": "\"\"", "rename": "true", "chain": "false", "sec_default": "{\"conditional_mask\": {\"__current_case__\": 0, \"selector\": \"disabled\"}, \"iupac_codes\": false, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"mask\": {\"values\": [{\"id\": 267, \"src\": \"hda\"}]}, \"sample\": null, \"select_haplotype\": null}", "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 266, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_file": {"id": "652697a80da4fc96", "src": "hda", "uuid": "0a142ea4-6eb4-4686-a39b-061a3411d5ae"}, "reference_source|fasta_ref": {"id": "b4e272fcf3820c05", "src": "hda", "uuid": "11779aa8-a59d-4c23-b5d6-0bc41cd1fbc1"}, "sec_default|mask": {"id": "f5609ab2bcfa2ba6", "src": "hda", "uuid": "531c5a98-4a25-479b-9a1a-dd7722717660"}}, "outputs": {"output_file": {"id": "3b6657b4b98b5992", "src": "hda", "uuid": "814f42c2-903c-4568-b6fd-f72a31e56241"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 12 variants\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 12 variants\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-25 19:39:48", "plugin": "core", "name": "end_epoch", "raw_value": "1727293188.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:39:48", "plugin": "core", "name": "start_epoch", "raw_value": "1727293188.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_consensus/1.15.1+galaxy4-3", "has_data": true, "data": {"tool_id": "bcftools_consensus", "tool_version": "1.15.1+galaxy4", "test_index": 3, "time_seconds": 39.40394926071167, "inputs": {"input_file": {"src": "hda", "id": "1fbf4671315e09a4"}, "reference_source|fasta_ref": {"src": "hda", "id": "9230a47229dd5b9c"}, "reference_source|reference_source_selector": "history", "sec_restrict|include": "TYPE=\"snp\""}, "job": {"model_class": "Job", "id": "0a10c9179e291645", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:40:25.604043", "update_time": "2024-09-25T19:40:41.013670", "galaxy_version": "24.1", "external_id": "gxy-ccw2k", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/e/5/1/dataset_e51f3120-4493-4f3c-818b-d354b61fb34f.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/e/d/7/dataset_ed7f9af2-c8e3-4b29-b172-eadf40166fab.dat' ref.fa && samtools faidx ref.fa && bcftools consensus --fasta-ref ref.fa --include 'TYPE=\"snp\"' --output '/galaxy/server/database/objects/e/f/d/dataset_efd9feb6-4156-4088-85a0-d125b8bba3d9.dat' input.vcf.gz", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_restrict": "{\"exclude\": null, \"include\": \"TYPE=\\\"snp\\\"\"}", "absent": "\"\"", "rename": "false", "chain": "false", "sec_default": "{\"conditional_mask\": {\"__current_case__\": 0, \"selector\": \"disabled\"}, \"iupac_codes\": false, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"mask\": null, \"sample\": null, \"select_haplotype\": null}", "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 270, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_file": {"id": "1fbf4671315e09a4", "src": "hda", "uuid": "e51f3120-4493-4f3c-818b-d354b61fb34f"}, "reference_source|fasta_ref": {"id": "9230a47229dd5b9c", "src": "hda", "uuid": "ed7f9af2-c8e3-4b29-b172-eadf40166fab"}}, "outputs": {"output_file": {"id": "31bc614edd85d40d", "src": "hda", "uuid": "efd9feb6-4156-4088-85a0-d125b8bba3d9"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 6 variants\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 6 variants\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:40:28", "plugin": "core", "name": "end_epoch", "raw_value": "1727293228.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:40:27", "plugin": "core", "name": "start_epoch", "raw_value": "1727293227.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_consensus/1.15.1+galaxy4-4", "has_data": true, "data": {"tool_id": "bcftools_consensus", "tool_version": "1.15.1+galaxy4", "test_index": 4, "time_seconds": 30.043429613113403, "inputs": {"input_file": {"src": "hda", "id": "9d24a7dcc9e55344"}, "reference_source|fasta_ref": {"src": "hda", "id": "7a7325487ad2c378"}, "reference_source|reference_source_selector": "history", "absent": "W", "sec_restrict|include": "TYPE=\"snp\""}, "job": {"model_class": "Job", "id": "485eb734f0ba54cf", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4", "state": "error", "exit_code": null, "create_time": "2024-09-25T19:41:05.832557", "update_time": "2024-09-25T19:41:11.148060", "galaxy_version": "24.1", "external_id": "gxy-chmbv", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/6/f/b/dataset_6fb4252f-5187-4e87-911a-98c86cb1bee5.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/d/4/4/dataset_d44efd32-fcc4-4a55-9a92-6d6b03bc9836.dat' ref.fa && samtools faidx ref.fa && bcftools consensus --fasta-ref ref.fa --include 'TYPE=\"snp\"' --absent 'W' --output '/galaxy/server/database/objects/d/7/f/dataset_d7fb38a6-075c-42eb-93f3-e351e4456e28.dat' input.vcf.gz", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_restrict": "{\"exclude\": null, \"include\": \"TYPE=\\\"snp\\\"\"}", "absent": "\"W\"", "rename": "false", "chain": "false", "sec_default": "{\"conditional_mask\": {\"__current_case__\": 0, \"selector\": \"disabled\"}, \"iupac_codes\": false, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"mask\": null, \"sample\": null, \"select_haplotype\": null}", "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 273, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_file": {"id": "9d24a7dcc9e55344", "src": "hda", "uuid": "6fb4252f-5187-4e87-911a-98c86cb1bee5"}, "reference_source|fasta_ref": {"id": "7a7325487ad2c378", "src": "hda", "uuid": "d44efd32-fcc4-4a55-9a92-6d6b03bc9836"}}, "outputs": {"output_file": {"id": "d21c8ecbbf22e9c2", "src": "hda", "uuid": "d7fb38a6-075c-42eb-93f3-e351e4456e28"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 6 variants\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 6 variants\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, exit_code: None, stderr: Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 6 variants\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4, exit_code: None, stderr: Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 6 variants\n."], "status": "failure"}}, {"id": "bcftools_consensus/1.15.1+galaxy4-5", "has_data": true, "data": {"tool_id": "bcftools_consensus", "tool_version": "1.15.1+galaxy4", "test_index": 5, "time_seconds": 40.2953462600708, "inputs": {"input_file": {"src": "hda", "id": "a54ad8eddb08db90"}, "reference_source|fasta_ref": {"src": "hda", "id": "f413acd23588bc01"}, "reference_source|reference_source_selector": "history", "sec_default|mark_del": "DEL", "sec_default|mark_ins": "uc", "sec_default|mark_snv": "uc", "sec_restrict|include": "TYPE=\"snp\""}, "job": {"model_class": "Job", "id": "de07d76736f6504c", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:41:35.509234", "update_time": "2024-09-25T19:41:51.391998", "galaxy_version": "24.1", "external_id": "gxy-4p8h2", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/4/4/8/dataset_448511e1-481b-4378-b4bc-e9056dbfa346.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/d/a/b/dataset_dab3d287-71c2-4a87-bfdf-218916f15953.dat' ref.fa && samtools faidx ref.fa && bcftools consensus --fasta-ref ref.fa --mark-del 'DEL' --mark-ins uc --mark-snv uc --include 'TYPE=\"snp\"' --output '/galaxy/server/database/objects/8/0/0/dataset_80072bea-9d41-4a03-a041-3104fa2eb9ab.dat' input.vcf.gz", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_restrict": "{\"exclude\": null, \"include\": \"TYPE=\\\"snp\\\"\"}", "absent": "\"\"", "rename": "false", "chain": "false", "sec_default": "{\"conditional_mask\": {\"__current_case__\": 0, \"selector\": \"disabled\"}, \"iupac_codes\": false, \"mark_del\": \"DEL\", \"mark_ins\": \"uc\", \"mark_snv\": \"uc\", \"mask\": null, \"sample\": null, \"select_haplotype\": null}", "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 276, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_file": {"id": "a54ad8eddb08db90", "src": "hda", "uuid": "448511e1-481b-4378-b4bc-e9056dbfa346"}, "reference_source|fasta_ref": {"id": "f413acd23588bc01", "src": "hda", "uuid": "dab3d287-71c2-4a87-bfdf-218916f15953"}}, "outputs": {"output_file": {"id": "445f0f16837541f6", "src": "hda", "uuid": "80072bea-9d41-4a03-a041-3104fa2eb9ab"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 6 variants\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 6 variants\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:41:38", "plugin": "core", "name": "end_epoch", "raw_value": "1727293298.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:41:37", "plugin": "core", "name": "start_epoch", "raw_value": "1727293297.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_plugin_impute_info/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_plugin_impute_info", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 43.98810362815857, "inputs": {"input_file": {"src": "hda", "id": "ba0b3933092f6b29"}, "output_type": "v"}, "job": {"model_class": "Job", "id": "c72c7cd141ddbde7", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:42:16.122484", "update_time": "2024-09-25T19:42:36.316455", "galaxy_version": "24.1", "external_id": "gxy-m5t77", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/a/9/9/dataset_a99e8e23-d3ef-475f-8bca-05a7093450d0.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin impute-info --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/4/2/0/dataset_42043258-f4f0-46cd-8166-f85f94c70b13.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_restrict": "{\"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_file": {"id": "ba0b3933092f6b29", "src": "hda", "uuid": "a99e8e23-d3ef-475f-8bca-05a7093450d0"}}, "outputs": {"output_file": {"id": "83bf61e51a3fb58d", "src": "hda", "uuid": "42043258-f4f0-46cd-8166-f85f94c70b13"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[impute-info.c] Warning: info tag not added to sites that are not biallelic diploid\nLines total/info-added/unchanged-no-tag/unchanged-not-biallelic-diploid:\t33/32/0/1\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[impute-info.c] Warning: info tag not added to sites that are not biallelic diploid\nLines total/info-added/unchanged-no-tag/unchanged-not-biallelic-diploid:\t33/32/0/1\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:42:22", "plugin": "core", "name": "end_epoch", "raw_value": "1727293342.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:42:21", "plugin": "core", "name": "start_epoch", "raw_value": "1727293341.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_query/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_query", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 39.18650436401367, "inputs": {"input_files": {"src": "hda", "id": "bc1dafc9df43479d"}, "sec_query|format": "%CHROM\\t%POS\\t%REF\\t%ALT\\t%DP4\\t%AN[\\t%GT\\t%TGT]\\n", "sec_query|tsv": true}, "job": {"model_class": "Job", "id": "7a621d657db1f4b9", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:43:01.299622", "update_time": "2024-09-25T19:43:16.444198", "galaxy_version": "24.1", "external_id": "gxy-zs9wx", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/2/3/5/dataset_2354e558-fab9-410f-8ecb-308738957990.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bcftools query --format '%CHROM\\t%POS\\t%REF\\t%ALT\\t%DP4\\t%AN[\\t%GT\\t%TGT]\\n' --vcf-list vcfs_list > /galaxy/server/database/objects/7/f/3/dataset_7f3a2b48-00f3-4471-ad3d-7a748b3e4ca8.dat", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_query": "{\"allow_undef_tags\": false, \"format\": \"%CHROM\\\\t%POS\\\\t%REF\\\\t%ALT\\\\t%DP4\\\\t%AN[\\\\t%GT\\\\t%TGT]\\\\n\", \"print_header\": false, \"tsv\": true}", "sec_restrict": "{\"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_files": {"id": "bc1dafc9df43479d", "src": "hda", "uuid": "2354e558-fab9-410f-8ecb-308738957990"}, "input_files1": {"id": "bc1dafc9df43479d", "src": "hda", "uuid": "2354e558-fab9-410f-8ecb-308738957990"}}, "outputs": {"output_file": {"id": "32773e0a3dae9d46", "src": "hda", "uuid": "7f3a2b48-00f3-4471-ad3d-7a748b3e4ca8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-25 19:43:03", "plugin": "core", "name": "end_epoch", "raw_value": "1727293383.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:43:03", "plugin": "core", "name": "start_epoch", "raw_value": "1727293383.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_query/1.15.1+galaxy4-1", "has_data": true, "data": {"tool_id": "bcftools_query", "tool_version": "1.15.1+galaxy4", "test_index": 1, "time_seconds": 39.459524631500244, "inputs": {"input_files": {"src": "hda", "id": "e43c19d0f48027b9"}, "sec_restrict|regions_overlap": "1", "sec_query|format": "%CHROM\\t%POS\\t%REF\\t%ALT\\t%DP4\\t%AN[\\t%GT\\t%TGT]\\n", "sec_query|tsv": true}, "job": {"model_class": "Job", "id": "b98785ad821d01f5", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:43:40.106462", "update_time": "2024-09-25T19:43:55.920261", "galaxy_version": "24.1", "external_id": "gxy-mskqx", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/4/e/7/dataset_4e7d3408-7f55-41e5-b887-f27f9509f7d0.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bcftools query --format '%CHROM\\t%POS\\t%REF\\t%ALT\\t%DP4\\t%AN[\\t%GT\\t%TGT]\\n' --regions-overlap 1 --vcf-list vcfs_list > /galaxy/server/database/objects/7/8/5/dataset_7859ad20-3ced-4d31-8e2e-1b591fcef974.dat", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_query": "{\"allow_undef_tags\": false, \"format\": \"%CHROM\\\\t%POS\\\\t%REF\\\\t%ALT\\\\t%DP4\\\\t%AN[\\\\t%GT\\\\t%TGT]\\\\n\", \"print_header\": false, \"tsv\": true}", "sec_restrict": "{\"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": \"1\", \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}"}, "inputs": {"input_files": {"id": "e43c19d0f48027b9", "src": "hda", "uuid": "4e7d3408-7f55-41e5-b887-f27f9509f7d0"}, "input_files1": {"id": "e43c19d0f48027b9", "src": "hda", "uuid": "4e7d3408-7f55-41e5-b887-f27f9509f7d0"}}, "outputs": {"output_file": {"id": "2ee92309e1ad76d8", "src": "hda", "uuid": "7859ad20-3ced-4d31-8e2e-1b591fcef974"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-25 19:43:42", "plugin": "core", "name": "end_epoch", "raw_value": "1727293422.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:43:42", "plugin": "core", "name": "start_epoch", "raw_value": "1727293422.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "circos/0.69.8+galaxy7-0", "has_data": true, "data": {"tool_id": "circos", "tool_version": "0.69.8+galaxy7", "test_index": 0, "time_seconds": 69.46436429023743, "inputs": {"reference_genome|ref|genome_fasta": {"src": "hda", "id": "8f780dea779801ec"}, "reference_genome|ref|ref_source": "history", "outputs|png": true, "outputs|svg": true}, "job": {"model_class": "Job", "id": "9a23fa6d55ec7058", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T18:36:51.989493", "update_time": "2024-09-25T18:37:38.555149", "galaxy_version": "24.1", "external_id": "gxy-ck88b", "handler": null, "job_runner_name": null, "command_line": "mkdir -p circos/conf/ circos/data/ && ln -s '/galaxy/server/database/objects/b/e/1/dataset_be12adf2-996d-4df4-89a1-08d35c4956ba.dat' genomeref.fa && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/circos/df7356989ac1/circos/karyotype-from-fasta.py' genomeref.fa > circos/conf/karyotype.txt && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/circos/df7356989ac1/circos/karyotype-colors.py' `grep -c '^chr\\s' 'circos/conf/karyotype.txt'` > 'circos/conf/karyotype-colors.conf' && touch circos/conf/karyotype-colors.conf && cp '/galaxy/server/database/jobs_directory/000/14/configs/tmpam9xai6f' circos/conf/circos.conf && cp '/galaxy/server/database/jobs_directory/000/14/configs/tmpwk2dojf0' circos/conf/ticks.conf && cp '/galaxy/server/database/jobs_directory/000/14/configs/tmp_q2hqggv' circos/conf/ideogram.conf && cp '/galaxy/server/database/jobs_directory/000/14/configs/tmp_bsgbdiz' circos/conf/data.conf && cp '/galaxy/server/database/jobs_directory/000/14/configs/tmpgedrcc8r' circos/conf/links.conf && cp '/galaxy/server/database/jobs_directory/000/14/configs/tmpr5kz2hpd' circos/conf/galaxy_test_case.json && circos -conf circos/conf/circos.conf -noparanoid", "user_email": "tests@fake.org", "command_version": "circos | v 0.69-8 | 15 Jun 2019 | Perl 5.026002", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "outputs": "{\"png\": true, \"svg\": true, \"tar\": false}", "limits": "{\"max_ideograms\": \"200\", \"max_links\": \"25000\", \"max_points_per_track\": \"25000\", \"max_ticks\": \"5000\"}", "ticks": "{\"radius\": \"1.0\", \"skip_first_label\": false, \"skip_last_label\": false, \"tick_group\": []}", "scaling": "{\"zooms\": []}", "sec_links": "{\"data\": []}", "sec_tdd": "{\"data\": []}", "plot_options": "{\"background\": {\"__current_case__\": 1, \"background_color\": \"#ffffff\", \"background_select\": \"color\"}, \"colour_profile\": null, \"radius\": \"1500\"}", "ideogram": "{\"angle_offset\": \"-90\", \"angle_orientation\": \"clockwise\", \"bands\": {\"band_stroke_color\": \"#000000\", \"band_stroke_thickness\": \"0\", \"band_transparency\": \"3\", \"fill_bands\": true, \"show_bands\": true}, \"chromosomes_reverse\": null, \"ideogram_labels\": {\"parallel\": true, \"radius_offset\": \"0.075\", \"show_label\": true, \"size\": \"24\"}, \"limit_chromosomes\": null, \"pairwise_spacing\": [], \"radius\": \"0.9\", \"spacing\": \"0.5\", \"thickness\": \"30.0\", \"units\": \"mb\"}", "reference_genome": "{\"ref\": {\"__current_case__\": 2, \"genome_fasta\": {\"values\": [{\"id\": 22, \"src\": \"hda\"}]}, \"ref_source\": \"history\"}}"}, "inputs": {"reference_genome|ref|genome_fasta": {"id": "8f780dea779801ec", "src": "hda", "uuid": "be12adf2-996d-4df4-89a1-08d35c4956ba"}}, "outputs": {"output_png": {"id": "fec0cc1329409cb5", "src": "hda", "uuid": "647145be-4c33-4297-9ac3-57e872881b95"}, "output_svg": {"id": "8b62c289ec63f46c", "src": "hda", "uuid": "3c923db1-4fad-4831-8365-dedbfae6d739"}, "karyotype_txt": {"id": "0e987f15c922d142", "src": "hda", "uuid": "d1493d9c-b6c5-4a6d-931f-8ea4154b1280"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "debuggroup summary 0.18s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002\ndebuggroup summary 0.18s current working directory /galaxy/server/database/jobs_directory/000/14/working\ndebuggroup summary 0.18s command /usr/local/bin/circos -conf circos/conf/circos.conf -noparanoid\ndebuggroup summary 0.18s loading configuration from file circos/conf/circos.conf\ndebuggroup summary 0.19s found conf file circos/conf/circos.conf\ndebuggroup summary 0.34s debug will appear for these features: output,summary\ndebuggroup summary 0.34s bitmap output image ./circos.png\ndebuggroup summary 0.34s SVG output image ./circos.svg\ndebuggroup summary 0.34s parsing karyotype and organizing ideograms\ndebuggroup summary 0.34s karyotype has 2 chromosomes of total size 56,082\ndebuggroup summary 0.34s applying global and local scaling\ndebuggroup summary 0.34s allocating image, colors and brushes\ndebuggroup summary 7.32s drawing 2 ideograms of total size 56,082\ndebuggroup summary 7.32s drawing highlights and ideograms\ndebuggroup output 7.33s generating output\ndebuggroup output 7.78s created PNG image ./circos.png (40 kb)\ndebuggroup output 7.78s created SVG image ./circos.svg (2 kb)\n", "tool_stderr": "Use of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\n", "job_stdout": "", "job_stderr": "", "stdout": "debuggroup summary 0.18s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002\ndebuggroup summary 0.18s current working directory /galaxy/server/database/jobs_directory/000/14/working\ndebuggroup summary 0.18s command /usr/local/bin/circos -conf circos/conf/circos.conf -noparanoid\ndebuggroup summary 0.18s loading configuration from file circos/conf/circos.conf\ndebuggroup summary 0.19s found conf file circos/conf/circos.conf\ndebuggroup summary 0.34s debug will appear for these features: output,summary\ndebuggroup summary 0.34s bitmap output image ./circos.png\ndebuggroup summary 0.34s SVG output image ./circos.svg\ndebuggroup summary 0.34s parsing karyotype and organizing ideograms\ndebuggroup summary 0.34s karyotype has 2 chromosomes of total size 56,082\ndebuggroup summary 0.34s applying global and local scaling\ndebuggroup summary 0.34s allocating image, colors and brushes\ndebuggroup summary 7.32s drawing 2 ideograms of total size 56,082\ndebuggroup summary 7.32s drawing highlights and ideograms\ndebuggroup output 7.33s generating output\ndebuggroup output 7.78s created PNG image ./circos.png (40 kb)\ndebuggroup output 7.78s created SVG image ./circos.svg (2 kb)\n", "stderr": "Use of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "10737", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "10737.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:37:12", "plugin": "core", "name": "start_epoch", "raw_value": "1727289432.0000000"}, {"title": "Job End Time", "value": "2024-09-25 18:37:21", "plugin": "core", "name": "end_epoch", "raw_value": "1727289441.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "9 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "9.0000000"}]}, "status": "success"}}, {"id": "circos/0.69.8+galaxy7-1", "has_data": true, "data": {"tool_id": "circos", "tool_version": "0.69.8+galaxy7", "test_index": 1, "time_seconds": 14.174577713012695, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "deeptools_multi_bam_summary/3.5.4+galaxy0-0", "has_data": true, "data": {"tool_id": "deeptools_multi_bam_summary", "tool_version": "3.5.4+galaxy0", "test_index": 0, "time_seconds": 90.2899100780487, "inputs": {"multibam_conditional|bamfiles": [{"src": "hda", "id": "beda644706419afa"}, {"src": "hda", "id": "beda644706419afa"}], "mode|binSize": "10", "mode|modeOpt": "bins"}, "job": {"model_class": "Job", "id": "b57d210239bedb57", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T18:32:36.342714", "update_time": "2024-09-25T18:33:36.594139", "galaxy_version": "24.1", "external_id": "gxy-n442z", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/7/e/5/dataset_7e52a667-844c-4527-951d-8844cd4751a2.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/9/b/c/metadata_9bcaba97-6eeb-41e9-b6b6-6864e347f28e.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/7/e/5/dataset_7e52a667-844c-4527-951d-8844cd4751a2.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/9/b/c/metadata_9bcaba97-6eeb-41e9-b6b6-6864e347f28e.dat' './1.bam.bai' && multiBamSummary bins --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --outFileName '/galaxy/server/database/objects/6/a/e/dataset_6ae7ebd1-8479-4033-b3f2-89db4d58d6ca.dat' --bamfiles '0.bam' '1.bam' --labels 'bowtie2 test1.bam' 'bowtie2 test1.bam' --binSize '10' --distanceBetweenBins '0'", "user_email": "tests@fake.org", "command_version": "multiBamSummary 3.5.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "scalingFactors": "false", "outRawCounts": "false", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "region": "\"\"", "mode": "{\"__current_case__\": 0, \"binSize\": \"10\", \"distanceBetweenBins\": \"0\", \"modeOpt\": \"bins\"}", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibam_conditional": "{\"__current_case__\": 0, \"bamfiles\": {\"values\": [{\"id\": 1, \"src\": \"hda\"}, {\"id\": 1, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}"}, "inputs": {"multibam_conditional|bamfiles2": {"id": "beda644706419afa", "src": "hda", "uuid": "7e52a667-844c-4527-951d-8844cd4751a2"}, "multibam_conditional|bamfiles1": {"id": "beda644706419afa", "src": "hda", "uuid": "7e52a667-844c-4527-951d-8844cd4751a2"}, "multibam_conditional|bamfiles": {"id": "beda644706419afa", "src": "hda", "uuid": "7e52a667-844c-4527-951d-8844cd4751a2"}}, "outputs": {"outFile": {"id": "b57d210239bedb57", "src": "hda", "uuid": "6ae7ebd1-8479-4033-b3f2-89db4d58d6ca"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of bins found: 1657\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Number of bins found: 1657\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-25 18:33:20", "plugin": "core", "name": "end_epoch", "raw_value": "1727289200.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:33:18", "plugin": "core", "name": "start_epoch", 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"2024-09-25T18:34:01.118463", "update_time": "2024-09-25T18:34:17.122132", "galaxy_version": "24.1", "external_id": "gxy-khnlj", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/0/e/0/dataset_0e019ee3-2372-4f9c-89c7-e644011259db.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/0/6/f/metadata_06f7d41d-cd43-4e53-a468-4cd5cd1c8f32.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/0/e/0/dataset_0e019ee3-2372-4f9c-89c7-e644011259db.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/0/6/f/metadata_06f7d41d-cd43-4e53-a468-4cd5cd1c8f32.dat' './1.bam.bai' && multiBamSummary BED-file --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --outFileName '/galaxy/server/database/objects/3/3/c/dataset_33c216dc-73a8-4f54-83e1-510c2178b7a8.dat' --bamfiles '0.bam' '1.bam' --labels 'bowtie2 test1.bam' 'bowtie2 test1.bam' --BED 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'/galaxy/server/database/objects/6/8/d/dataset_68d10d54-d722-477f-ac81-8b3c71b5e425.dat' > '/galaxy/server/database/objects/a/2/9/dataset_a2998b24-d706-4bab-8187-fdf2fd19437b.dat'; sed -e 's/@@title@@/Diff report for \"file1.txt\" and \"file2.txt\"/g' -e 's/@@outputformat@@/'side-by-side'/g' -e '/@@diffoutput@@/{r'/galaxy/server/database/objects/a/2/9/dataset_a2998b24-d706-4bab-8187-fdf2fd19437b.dat'' -e ';d}' '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/diff/156d0908e232/diff/template.html' > '/galaxy/server/database/objects/5/2/6/dataset_5269577a-6c11-4b22-a0d6-8a23b2dcad49.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_format": "\"side-by-side\"", "generate_report": "true"}, "inputs": {"input1": {"id": "411b50cb3616d699", "src": "hda", "uuid": "4e074501-ae5e-4e85-a4b5-fcc6145a1bee"}, "input2": {"id": 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null, "command_line": "diff -u '/galaxy/server/database/objects/a/8/b/dataset_a8b35562-68b0-4fe6-b13a-8dce62769cb9.dat' '/galaxy/server/database/objects/b/2/0/dataset_b2009806-1e07-49d0-9e5f-4b40330e76db.dat' > '/galaxy/server/database/objects/4/5/4/dataset_4549efc6-c477-42bf-ab72-ed3a519bb611.dat'; sed -e 's/@@title@@/Diff report for \"file1.txt\" and \"file2.txt\"/g' -e 's/@@outputformat@@/'line-by-line'/g' -e '/@@diffoutput@@/{r'/galaxy/server/database/objects/4/5/4/dataset_4549efc6-c477-42bf-ab72-ed3a519bb611.dat'' -e ';d}' '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/diff/156d0908e232/diff/template.html' > '/galaxy/server/database/objects/8/6/c/dataset_86cc1c8d-40d7-4b64-8c2c-62d3e7d6c78b.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_format": "\"line-by-line\"", "generate_report": "true"}, "inputs": {"input1": {"id": "b0f72cfe0db71b5b", "src": "hda", "uuid": "a8b35562-68b0-4fe6-b13a-8dce62769cb9"}, "input2": {"id": "e740c898d46a3bec", "src": "hda", "uuid": "b2009806-1e07-49d0-9e5f-4b40330e76db"}}, "outputs": {"diff_file": {"id": "520233e96dd6dd50", "src": "hda", "uuid": "4549efc6-c477-42bf-ab72-ed3a519bb611"}, "html_file": {"id": "3b98487d11d1df0a", "src": "hda", "uuid": "86cc1c8d-40d7-4b64-8c2c-62d3e7d6c78b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-25 19:37:43", "plugin": "core", "name": "end_epoch", "raw_value": "1727293063.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:37:43", "plugin": "core", "name": "start_epoch", "raw_value": "1727293063.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "diff/3.7+galaxy0-5", "has_data": true, "data": {"tool_id": "diff", "tool_version": "3.7+galaxy0", "test_index": 5, "time_seconds": 28.768495082855225, "inputs": {"input1": {"src": "hda", "id": "225d5899908dbd3e"}, "input2": {"src": "hda", "id": "225d5899908dbd3e"}, "generate_report": true}, "job": {"model_class": "Job", "id": "10c52727a6cf2bc6", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0", "state": "error", "exit_code": null, "create_time": "2024-09-25T19:38:19.713458", "update_time": "2024-09-25T19:38:25.306243", "galaxy_version": "24.1", "external_id": "gxy-r4r55", "handler": null, "job_runner_name": null, "command_line": "diff -u '/galaxy/server/database/objects/9/4/8/dataset_94818178-a034-419c-b3e2-d7f0fafb1861.dat' '/galaxy/server/database/objects/9/4/8/dataset_94818178-a034-419c-b3e2-d7f0fafb1861.dat' > '/galaxy/server/database/objects/9/8/9/dataset_98993230-2033-44e0-a793-95e7771ffbb8.dat'; sed -e 's/@@title@@/Diff report for \"file 3.txt\" and \"file 3.txt\"/g' -e 's/@@outputformat@@/'side-by-side'/g' -e '/@@diffoutput@@/{r'/galaxy/server/database/objects/9/8/9/dataset_98993230-2033-44e0-a793-95e7771ffbb8.dat'' -e ';d}' '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/diff/156d0908e232/diff/template.html' > '/galaxy/server/database/objects/3/2/c/dataset_32c26dc8-bc80-4d21-a614-54f50496d495.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_format": "\"side-by-side\"", "generate_report": "true"}, "inputs": {"input1": {"id": "225d5899908dbd3e", "src": "hda", "uuid": "94818178-a034-419c-b3e2-d7f0fafb1861"}, "input2": {"id": "225d5899908dbd3e", "src": "hda", "uuid": "94818178-a034-419c-b3e2-d7f0fafb1861"}}, "outputs": {"diff_file": {"id": "24eb12e4dc7da3c5", "src": "hda", "uuid": "98993230-2033-44e0-a793-95e7771ffbb8"}, "html_file": {"id": "735adcc660abafa2", "src": "hda", "uuid": "32c26dc8-bc80-4d21-a614-54f50496d495"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, exit_code: None, stderr: .", "Expected job to complete with exit code 0, found None", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "fastq_paired_end_deinterlacer/1.1.5-0", "has_data": true, "data": {"tool_id": "fastq_paired_end_deinterlacer", "tool_version": "1.1.5", "test_index": 0, "time_seconds": 44.015777826309204, "inputs": {"input_file": {"src": "hda", "id": "a54abfa9c7160f6d"}}, "job": {"model_class": "Job", "id": "9138e2b6fba36894", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T18:34:40.765936", "update_time": "2024-09-25T18:35:00.953100", "galaxy_version": "24.1", "external_id": "gxy-d6mks", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-paired-end-deinterlacer '/galaxy/server/database/objects/6/c/d/dataset_6cd465c8-d857-4083-bd90-c163ec99a758.dat' 'sanger' '/galaxy/server/database/objects/6/4/2/dataset_642e001b-bba9-40a6-9f80-ea5801f2e73d.dat' '/galaxy/server/database/objects/9/2/9/dataset_9298a47e-ac01-4f14-8429-881354ad031e.dat' '/galaxy/server/database/objects/6/0/7/dataset_6079acb4-6ca1-4633-bf70-a4a5c7348d88.dat' '/galaxy/server/database/objects/6/e/c/dataset_6ec70fda-bd20-49bc-8587-e66b8714155f.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fastqsanger\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input_file": {"id": "a54abfa9c7160f6d", "src": "hda", "uuid": "6cd465c8-d857-4083-bd90-c163ec99a758"}}, "outputs": {"output2_singles_file": {"id": "c99a2d897e0b2e76", "src": "hda", "uuid": "6ec70fda-bd20-49bc-8587-e66b8714155f"}, "output1_singles_file": {"id": "94da987fbf0a05eb", "src": "hda", "uuid": "6079acb4-6ca1-4633-bf70-a4a5c7348d88"}, "output2_pairs_file": {"id": "f6e2a75ac3682018", "src": "hda", "uuid": "9298a47e-ac01-4f14-8429-881354ad031e"}, "output1_pairs_file": {"id": "9138e2b6fba36894", "src": "hda", "uuid": "642e001b-bba9-40a6-9f80-ea5801f2e73d"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "De-interlaced 5.0 pairs of sequences.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "De-interlaced 5.0 pairs of sequences.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-25 18:34:46", "plugin": "core", "name": "end_epoch", "raw_value": "1727289286.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:34:46", "plugin": "core", "name": "start_epoch", "raw_value": "1727289286.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_paired_end_deinterlacer/1.1.5-1", "has_data": true, "data": {"tool_id": "fastq_paired_end_deinterlacer", "tool_version": "1.1.5", "test_index": 1, "time_seconds": 12.381095886230469, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "fastq_paired_end_deinterlacer/1.1.5-2", "has_data": true, "data": {"tool_id": "fastq_paired_end_deinterlacer", "tool_version": "1.1.5", "test_index": 2, "time_seconds": 36.81135010719299, "inputs": {"input_file": {"src": "hda", "id": "50e89d1f095adcdd"}}, "job": {"model_class": "Job", "id": "c99a2d897e0b2e76", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T18:35:36.561327", "update_time": "2024-09-25T18:35:50.318244", "galaxy_version": "24.1", "external_id": "gxy-gwj58", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-paired-end-deinterlacer '/galaxy/server/database/objects/6/c/f/dataset_6cf0efa9-7dea-4ceb-a617-334889c0770f.dat' 'sanger.gz' '/galaxy/server/database/objects/9/c/9/dataset_9c9b5365-763d-4c1f-bb4d-4ec91f739696.dat' '/galaxy/server/database/objects/6/4/d/dataset_64d79707-d188-4cbd-934b-79a77ac8a7a5.dat' '/galaxy/server/database/objects/4/9/5/dataset_49576436-bf41-420d-8d89-57a8c849522e.dat' '/galaxy/server/database/objects/e/e/8/dataset_ee89afaf-3baf-4630-b87f-2a1d7ad188cc.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastqsanger.gz\""}, "inputs": {"input_file": {"id": "50e89d1f095adcdd", "src": "hda", "uuid": "6cf0efa9-7dea-4ceb-a617-334889c0770f"}}, "outputs": {"output2_singles_file": {"id": "ee2b038af4efbd73", "src": "hda", "uuid": "ee89afaf-3baf-4630-b87f-2a1d7ad188cc"}, "output1_singles_file": {"id": "120c2a079f3eac9d", "src": "hda", "uuid": "49576436-bf41-420d-8d89-57a8c849522e"}, "output2_pairs_file": {"id": "9a23fa6d55ec7058", "src": "hda", "uuid": "64d79707-d188-4cbd-934b-79a77ac8a7a5"}, "output1_pairs_file": {"id": "b227b6c596552f96", "src": "hda", "uuid": "9c9b5365-763d-4c1f-bb4d-4ec91f739696"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "There were 2 reads with no mate.\nDe-interlaced 4.0 pairs of sequences.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "There were 2 reads with no mate.\nDe-interlaced 4.0 pairs of sequences.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-25 18:35:38", "plugin": "core", "name": "end_epoch", "raw_value": "1727289338.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:35:38", "plugin": "core", "name": "start_epoch", "raw_value": "1727289338.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_paired_end_deinterlacer/1.1.5-3", "has_data": true, "data": {"tool_id": "fastq_paired_end_deinterlacer", "tool_version": "1.1.5", "test_index": 3, "time_seconds": 37.20365285873413, "inputs": {"input_file": {"src": "hda", "id": "34339c52936f8125"}}, "job": {"model_class": "Job", "id": "50e89d1f095adcdd", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T18:36:12.821043", "update_time": "2024-09-25T18:36:27.661985", "galaxy_version": "24.1", "external_id": "gxy-m4d6f", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-paired-end-deinterlacer '/galaxy/server/database/objects/d/f/4/dataset_df481daf-9d29-4f02-ba42-dbb1e05ec27f.dat' 'sanger.bz2' '/galaxy/server/database/objects/8/8/b/dataset_88b152e4-738f-4c3d-a9d9-65579eed794f.dat' '/galaxy/server/database/objects/2/a/a/dataset_2aaa9d88-187c-4004-9a18-a1458c631a37.dat' '/galaxy/server/database/objects/4/9/8/dataset_498fe09a-9212-4a62-aed7-ce4c091101e4.dat' '/galaxy/server/database/objects/b/f/e/dataset_bfe88a80-2fc6-4853-ac30-4c78fd1f764e.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastqsanger.bz2\""}, "inputs": {"input_file": {"id": "34339c52936f8125", "src": "hda", "uuid": "df481daf-9d29-4f02-ba42-dbb1e05ec27f"}}, "outputs": {"output1_pairs_file": {"id": "41b1182783b897f9", "src": "hda", "uuid": "88b152e4-738f-4c3d-a9d9-65579eed794f"}, "output2_pairs_file": {"id": "c46d92a1e6cf00ac", "src": "hda", "uuid": "2aaa9d88-187c-4004-9a18-a1458c631a37"}, "output1_singles_file": {"id": "f1920e75c568676d", "src": "hda", "uuid": "498fe09a-9212-4a62-aed7-ce4c091101e4"}, "output2_singles_file": {"id": "ceb3bd7fc9c15f86", "src": "hda", "uuid": "bfe88a80-2fc6-4853-ac30-4c78fd1f764e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "There were 2 reads with no mate.\nDe-interlaced 4.0 pairs of sequences.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "There were 2 reads with no mate.\nDe-interlaced 4.0 pairs of sequences.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-25 18:36:15", "plugin": "core", "name": "end_epoch", "raw_value": "1727289375.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:36:15", "plugin": "core", "name": "start_epoch", "raw_value": "1727289375.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "ivar_trim/1.4.3+galaxy0-0", "has_data": true, "data": {"tool_id": "ivar_trim", "tool_version": "1.4.3+galaxy0", "test_index": 0, "time_seconds": 49.57129120826721, "inputs": {"input_bam": {"src": "hda", "id": "a236cf11c9879689"}, "primer|input_bed": {"src": "hda", "id": "1047ac6e568ddc62"}, "inc_primers": true, "trimmed_length|min_len": "30", "trimmed_length|filter": "custom"}, "job": {"model_class": "Job", "id": "f568b7247e833819", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:45:11.193912", "update_time": "2024-09-25T19:45:33.465547", "galaxy_version": "24.1", "external_id": "gxy-p8c72", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/2/6/4/dataset_26486f5e-b995-4496-8de7-8526c5e4806a.dat' bed.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/a250929be21b/ivar_trim/sanitize_bed.py' bed.bed && ln -s '/galaxy/server/database/objects/3/d/4/dataset_3d417bb4-2a73-401e-885a-36b5958aa8b0.dat' sorted.bam && ln -s '/galaxy/server/database/objects/_metadata_files/6/1/b/metadata_61b7be62-1f4a-45a1-a338-67d5022ffd9e.dat' sorted.bam.bai && ivar trim -i sorted.bam -b bed.bed -x 0 -e -m 30 -q 20 -s 4 | samtools sort -@ ${GALAXY_SLOTS:-1} -T \"${TMPDIR:-.}\" -o trimmed.sorted.bam -", "user_email": "tests@fake.org", "command_version": "iVar version 1.4.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "trimmed_length": "{\"__current_case__\": 2, \"filter\": \"custom\", \"min_len\": \"30\"}", "window_width": "\"4\"", "min_qual": "\"20\"", "inc_primers": "true", "primer_pos_wiggle": "\"0\"", "amplicons": "{\"__current_case__\": 2, \"filter_by\": \"\"}", "primer": "{\"__current_case__\": 0, \"input_bed\": {\"values\": [{\"id\": 288, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"input_bam": {"id": "a236cf11c9879689", "src": "hda", "uuid": "3d417bb4-2a73-401e-885a-36b5958aa8b0"}, "primer|input_bed": {"id": "1047ac6e568ddc62", "src": "hda", "uuid": "26486f5e-b995-4496-8de7-8526c5e4806a"}}, "outputs": {"output_bam": {"id": "d594dd91840942e4", "src": "hda", "uuid": "fbc23284-0c48-4e9c-a886-59b8352c5553"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Found 196 primers in BED file\nReading from sorted.bam\n\n-------\nResults: \nPrimer Name\tRead Count\nnCoV-2019_1_LEFT\t25\nnCoV-2019_1_RIGHT\t9\nnCoV-2019_2_LEFT\t10\nnCoV-2019_2_RIGHT\t17\nnCoV-2019_3_LEFT\t22\nnCoV-2019_3_RIGHT\t29\nnCoV-2019_4_LEFT\t20\nnCoV-2019_4_RIGHT\t5\nnCoV-2019_5_LEFT\t4\nnCoV-2019_5_RIGHT\t16\nnCoV-2019_6_LEFT\t17\nnCoV-2019_6_RIGHT\t10\nnCoV-2019_7_LEFT\t21\nnCoV-2019_7_RIGHT\t14\nnCoV-2019_8_LEFT\t5\nnCoV-2019_8_RIGHT\t10\nnCoV-2019_9_LEFT\t18\nnCoV-2019_9_RIGHT\t11\nnCoV-2019_10_LEFT\t20\nnCoV-2019_10_RIGHT\t11\nnCoV-2019_11_LEFT\t15\nnCoV-2019_11_RIGHT\t31\nnCoV-2019_12_LEFT\t48\nnCoV-2019_12_RIGHT\t11\nnCoV-2019_13_LEFT\t31\nnCoV-2019_13_RIGHT\t64\nnCoV-2019_14_LEFT\t53\nnCoV-2019_14_RIGHT\t89\nnCoV-2019_15_LEFT\t64\nnCoV-2019_15_RIGHT\t57\nnCoV-2019_16_LEFT\t168\nnCoV-2019_16_RIGHT\t112\nnCoV-2019_17_LEFT\t100\nnCoV-2019_17_RIGHT\t23\nnCoV-2019_18_LEFT\t19\nnCoV-2019_18_RIGHT\t42\nnCoV-2019_19_LEFT\t72\nnCoV-2019_19_RIGHT\t43\nnCoV-2019_20_LEFT\t31\nnCoV-2019_20_RIGHT\t63\nnCoV-2019_21_LEFT\t126\nnCoV-2019_21_RIGHT\t23\nnCoV-2019_22_LEFT\t55\nnCoV-2019_22_RIGHT\t58\nnCoV-2019_23_LEFT\t46\nnCoV-2019_23_RIGHT\t2\nnCoV-2019_24_LEFT\t22\nnCoV-2019_24_RIGHT\t6\nnCoV-2019_25_LEFT\t7\nnCoV-2019_25_RIGHT\t11\nnCoV-2019_26_LEFT\t13\nnCoV-2019_26_RIGHT\t14\nnCoV-2019_27_LEFT\t70\nnCoV-2019_27_RIGHT\t31\nnCoV-2019_28_LEFT\t15\nnCoV-2019_28_RIGHT\t6\nnCoV-2019_29_LEFT\t4\nnCoV-2019_29_RIGHT\t70\nnCoV-2019_30_LEFT\t10\nnCoV-2019_30_RIGHT\t26\nnCoV-2019_31_LEFT\t33\nnCoV-2019_31_RIGHT\t75\nnCoV-2019_32_LEFT\t119\nnCoV-2019_32_RIGHT\t52\nnCoV-2019_33_LEFT\t23\nnCoV-2019_33_RIGHT\t43\nnCoV-2019_34_LEFT\t51\nnCoV-2019_34_RIGHT\t40\nnCoV-2019_35_LEFT\t44\nnCoV-2019_35_RIGHT\t86\nnCoV-2019_36_LEFT\t113\nnCoV-2019_36_RIGHT\t131\nnCoV-2019_37_LEFT\t74\nnCoV-2019_37_RIGHT\t163\nnCoV-2019_38_LEFT\t185\nnCoV-2019_38_RIGHT\t113\nnCoV-2019_39_LEFT\t97\nnCoV-2019_39_RIGHT\t39\nnCoV-2019_40_LEFT\t67\nnCoV-2019_40_RIGHT\t17\nnCoV-2019_41_LEFT\t31\nnCoV-2019_41_RIGHT\t5\nnCoV-2019_42_LEFT\t39\nnCoV-2019_42_RIGHT\t89\nnCoV-2019_43_LEFT\t47\nnCoV-2019_43_RIGHT\t23\nnCoV-2019_44_LEFT\t51\nnCoV-2019_44_RIGHT\t70\nnCoV-2019_45_LEFT\t43\nnCoV-2019_45_RIGHT\t16\nnCoV-2019_46_LEFT\t11\nnCoV-2019_46_RIGHT\t35\nnCoV-2019_47_LEFT\t27\nnCoV-2019_47_RIGHT\t25\nnCoV-2019_48_LEFT\t74\nnCoV-2019_48_RIGHT\t41\nnCoV-2019_49_LEFT\t40\nnCoV-2019_49_RIGHT\t54\nnCoV-2019_50_LEFT\t26\nnCoV-2019_50_RIGHT\t19\nnCoV-2019_51_LEFT\t81\nnCoV-2019_51_RIGHT\t47\nnCoV-2019_52_LEFT\t33\nnCoV-2019_52_RIGHT\t28\nnCoV-2019_53_LEFT\t75\nnCoV-2019_53_RIGHT\t35\nnCoV-2019_54_LEFT\t44\nnCoV-2019_54_RIGHT\t13\nnCoV-2019_55_LEFT\t66\nnCoV-2019_55_RIGHT\t96\nnCoV-2019_56_LEFT\t35\nnCoV-2019_56_RIGHT\t69\nnCoV-2019_57_LEFT\t112\nnCoV-2019_57_RIGHT\t78\nnCoV-2019_58_LEFT\t15\nnCoV-2019_58_RIGHT\t6\nnCoV-2019_59_LEFT\t35\nnCoV-2019_59_RIGHT\t23\nnCoV-2019_60_LEFT\t22\nnCoV-2019_60_RIGHT\t19\nnCoV-2019_61_LEFT\t33\nnCoV-2019_61_RIGHT\t33\nnCoV-2019_62_LEFT\t16\nnCoV-2019_62_RIGHT\t17\nnCoV-2019_63_LEFT\t47\nnCoV-2019_63_RIGHT\t31\nnCoV-2019_64_LEFT\t6\nnCoV-2019_64_RIGHT\t8\nnCoV-2019_65_LEFT\t6\nnCoV-2019_65_RIGHT\t59\nnCoV-2019_66_LEFT\t29\nnCoV-2019_66_RIGHT\t2\nnCoV-2019_67_LEFT\t6\nnCoV-2019_67_RIGHT\t0\nnCoV-2019_68_LEFT\t8\nnCoV-2019_68_RIGHT\t9\nnCoV-2019_69_LEFT\t17\nnCoV-2019_69_RIGHT\t5\nnCoV-2019_70_LEFT\t0\nnCoV-2019_70_RIGHT\t1\nnCoV-2019_71_LEFT\t1\nnCoV-2019_71_RIGHT\t5\nnCoV-2019_72_LEFT\t7\nnCoV-2019_72_RIGHT\t4\nnCoV-2019_73_LEFT\t0\nnCoV-2019_73_RIGHT\t4\nnCoV-2019_74_LEFT\t0\nnCoV-2019_74_RIGHT\t0\nnCoV-2019_75_LEFT\t2\nnCoV-2019_75_RIGHT\t1\nnCoV-2019_76_LEFT\t2\nnCoV-2019_76_RIGHT\t13\nnCoV-2019_77_LEFT\t27\nnCoV-2019_77_RIGHT\t87\nnCoV-2019_78_LEFT\t63\nnCoV-2019_78_RIGHT\t23\nnCoV-2019_79_LEFT\t5\nnCoV-2019_79_RIGHT\t17\nnCoV-2019_80_LEFT\t92\nnCoV-2019_80_RIGHT\t33\nnCoV-2019_81_LEFT\t28\nnCoV-2019_81_RIGHT\t79\nnCoV-2019_82_LEFT\t150\nnCoV-2019_82_RIGHT\t50\nnCoV-2019_83_LEFT\t22\nnCoV-2019_83_RIGHT\t41\nnCoV-2019_84_LEFT\t32\nnCoV-2019_84_RIGHT\t50\nnCoV-2019_85_LEFT\t77\nnCoV-2019_85_RIGHT\t37\nnCoV-2019_86_LEFT\t54\nnCoV-2019_86_RIGHT\t30\nnCoV-2019_87_LEFT\t48\nnCoV-2019_87_RIGHT\t3\nnCoV-2019_88_LEFT\t58\nnCoV-2019_88_RIGHT\t91\nnCoV-2019_89_LEFT\t37\nnCoV-2019_89_RIGHT\t30\nnCoV-2019_90_LEFT\t28\nnCoV-2019_90_RIGHT\t21\nnCoV-2019_91_LEFT\t27\nnCoV-2019_91_RIGHT\t2\nnCoV-2019_92_LEFT\t9\nnCoV-2019_92_RIGHT\t14\nnCoV-2019_93_LEFT\t38\nnCoV-2019_93_RIGHT\t23\nnCoV-2019_94_LEFT\t116\nnCoV-2019_94_RIGHT\t55\nnCoV-2019_95_LEFT\t39\nnCoV-2019_95_RIGHT\t8\nnCoV-2019_96_LEFT\t24\nnCoV-2019_96_RIGHT\t17\nnCoV-2019_97_LEFT\t0\nnCoV-2019_97_RIGHT\t1\nnCoV-2019_98_LEFT\t2\nnCoV-2019_98_RIGHT\t2\n\nTrimmed primers from 13.29% (6871) of reads.\n3.5% (1811) of reads were quality trimmed below the minimum length of 30 bp and were not written to file.\n84.15% (43493) of reads started outside of primer regions. Since the -e flag was given, these reads were written to file.\n58.16% (30061) of reads had their insert size smaller than their read length\n[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Found 196 primers in BED file\nReading from sorted.bam\n\n-------\nResults: \nPrimer Name\tRead Count\nnCoV-2019_1_LEFT\t25\nnCoV-2019_1_RIGHT\t9\nnCoV-2019_2_LEFT\t10\nnCoV-2019_2_RIGHT\t17\nnCoV-2019_3_LEFT\t22\nnCoV-2019_3_RIGHT\t29\nnCoV-2019_4_LEFT\t20\nnCoV-2019_4_RIGHT\t5\nnCoV-2019_5_LEFT\t4\nnCoV-2019_5_RIGHT\t16\nnCoV-2019_6_LEFT\t17\nnCoV-2019_6_RIGHT\t10\nnCoV-2019_7_LEFT\t21\nnCoV-2019_7_RIGHT\t14\nnCoV-2019_8_LEFT\t5\nnCoV-2019_8_RIGHT\t10\nnCoV-2019_9_LEFT\t18\nnCoV-2019_9_RIGHT\t11\nnCoV-2019_10_LEFT\t20\nnCoV-2019_10_RIGHT\t11\nnCoV-2019_11_LEFT\t15\nnCoV-2019_11_RIGHT\t31\nnCoV-2019_12_LEFT\t48\nnCoV-2019_12_RIGHT\t11\nnCoV-2019_13_LEFT\t31\nnCoV-2019_13_RIGHT\t64\nnCoV-2019_14_LEFT\t53\nnCoV-2019_14_RIGHT\t89\nnCoV-2019_15_LEFT\t64\nnCoV-2019_15_RIGHT\t57\nnCoV-2019_16_LEFT\t168\nnCoV-2019_16_RIGHT\t112\nnCoV-2019_17_LEFT\t100\nnCoV-2019_17_RIGHT\t23\nnCoV-2019_18_LEFT\t19\nnCoV-2019_18_RIGHT\t42\nnCoV-2019_19_LEFT\t72\nnCoV-2019_19_RIGHT\t43\nnCoV-2019_20_LEFT\t31\nnCoV-2019_20_RIGHT\t63\nnCoV-2019_21_LEFT\t126\nnCoV-2019_21_RIGHT\t23\nnCoV-2019_22_LEFT\t55\nnCoV-2019_22_RIGHT\t58\nnCoV-2019_23_LEFT\t46\nnCoV-2019_23_RIGHT\t2\nnCoV-2019_24_LEFT\t22\nnCoV-2019_24_RIGHT\t6\nnCoV-2019_25_LEFT\t7\nnCoV-2019_25_RIGHT\t11\nnCoV-2019_26_LEFT\t13\nnCoV-2019_26_RIGHT\t14\nnCoV-2019_27_LEFT\t70\nnCoV-2019_27_RIGHT\t31\nnCoV-2019_28_LEFT\t15\nnCoV-2019_28_RIGHT\t6\nnCoV-2019_29_LEFT\t4\nnCoV-2019_29_RIGHT\t70\nnCoV-2019_30_LEFT\t10\nnCoV-2019_30_RIGHT\t26\nnCoV-2019_31_LEFT\t33\nnCoV-2019_31_RIGHT\t75\nnCoV-2019_32_LEFT\t119\nnCoV-2019_32_RIGHT\t52\nnCoV-2019_33_LEFT\t23\nnCoV-2019_33_RIGHT\t43\nnCoV-2019_34_LEFT\t51\nnCoV-2019_34_RIGHT\t40\nnCoV-2019_35_LEFT\t44\nnCoV-2019_35_RIGHT\t86\nnCoV-2019_36_LEFT\t113\nnCoV-2019_36_RIGHT\t131\nnCoV-2019_37_LEFT\t74\nnCoV-2019_37_RIGHT\t163\nnCoV-2019_38_LEFT\t185\nnCoV-2019_38_RIGHT\t113\nnCoV-2019_39_LEFT\t97\nnCoV-2019_39_RIGHT\t39\nnCoV-2019_40_LEFT\t67\nnCoV-2019_40_RIGHT\t17\nnCoV-2019_41_LEFT\t31\nnCoV-2019_41_RIGHT\t5\nnCoV-2019_42_LEFT\t39\nnCoV-2019_42_RIGHT\t89\nnCoV-2019_43_LEFT\t47\nnCoV-2019_43_RIGHT\t23\nnCoV-2019_44_LEFT\t51\nnCoV-2019_44_RIGHT\t70\nnCoV-2019_45_LEFT\t43\nnCoV-2019_45_RIGHT\t16\nnCoV-2019_46_LEFT\t11\nnCoV-2019_46_RIGHT\t35\nnCoV-2019_47_LEFT\t27\nnCoV-2019_47_RIGHT\t25\nnCoV-2019_48_LEFT\t74\nnCoV-2019_48_RIGHT\t41\nnCoV-2019_49_LEFT\t40\nnCoV-2019_49_RIGHT\t54\nnCoV-2019_50_LEFT\t26\nnCoV-2019_50_RIGHT\t19\nnCoV-2019_51_LEFT\t81\nnCoV-2019_51_RIGHT\t47\nnCoV-2019_52_LEFT\t33\nnCoV-2019_52_RIGHT\t28\nnCoV-2019_53_LEFT\t75\nnCoV-2019_53_RIGHT\t35\nnCoV-2019_54_LEFT\t44\nnCoV-2019_54_RIGHT\t13\nnCoV-2019_55_LEFT\t66\nnCoV-2019_55_RIGHT\t96\nnCoV-2019_56_LEFT\t35\nnCoV-2019_56_RIGHT\t69\nnCoV-2019_57_LEFT\t112\nnCoV-2019_57_RIGHT\t78\nnCoV-2019_58_LEFT\t15\nnCoV-2019_58_RIGHT\t6\nnCoV-2019_59_LEFT\t35\nnCoV-2019_59_RIGHT\t23\nnCoV-2019_60_LEFT\t22\nnCoV-2019_60_RIGHT\t19\nnCoV-2019_61_LEFT\t33\nnCoV-2019_61_RIGHT\t33\nnCoV-2019_62_LEFT\t16\nnCoV-2019_62_RIGHT\t17\nnCoV-2019_63_LEFT\t47\nnCoV-2019_63_RIGHT\t31\nnCoV-2019_64_LEFT\t6\nnCoV-2019_64_RIGHT\t8\nnCoV-2019_65_LEFT\t6\nnCoV-2019_65_RIGHT\t59\nnCoV-2019_66_LEFT\t29\nnCoV-2019_66_RIGHT\t2\nnCoV-2019_67_LEFT\t6\nnCoV-2019_67_RIGHT\t0\nnCoV-2019_68_LEFT\t8\nnCoV-2019_68_RIGHT\t9\nnCoV-2019_69_LEFT\t17\nnCoV-2019_69_RIGHT\t5\nnCoV-2019_70_LEFT\t0\nnCoV-2019_70_RIGHT\t1\nnCoV-2019_71_LEFT\t1\nnCoV-2019_71_RIGHT\t5\nnCoV-2019_72_LEFT\t7\nnCoV-2019_72_RIGHT\t4\nnCoV-2019_73_LEFT\t0\nnCoV-2019_73_RIGHT\t4\nnCoV-2019_74_LEFT\t0\nnCoV-2019_74_RIGHT\t0\nnCoV-2019_75_LEFT\t2\nnCoV-2019_75_RIGHT\t1\nnCoV-2019_76_LEFT\t2\nnCoV-2019_76_RIGHT\t13\nnCoV-2019_77_LEFT\t27\nnCoV-2019_77_RIGHT\t87\nnCoV-2019_78_LEFT\t63\nnCoV-2019_78_RIGHT\t23\nnCoV-2019_79_LEFT\t5\nnCoV-2019_79_RIGHT\t17\nnCoV-2019_80_LEFT\t92\nnCoV-2019_80_RIGHT\t33\nnCoV-2019_81_LEFT\t28\nnCoV-2019_81_RIGHT\t79\nnCoV-2019_82_LEFT\t150\nnCoV-2019_82_RIGHT\t50\nnCoV-2019_83_LEFT\t22\nnCoV-2019_83_RIGHT\t41\nnCoV-2019_84_LEFT\t32\nnCoV-2019_84_RIGHT\t50\nnCoV-2019_85_LEFT\t77\nnCoV-2019_85_RIGHT\t37\nnCoV-2019_86_LEFT\t54\nnCoV-2019_86_RIGHT\t30\nnCoV-2019_87_LEFT\t48\nnCoV-2019_87_RIGHT\t3\nnCoV-2019_88_LEFT\t58\nnCoV-2019_88_RIGHT\t91\nnCoV-2019_89_LEFT\t37\nnCoV-2019_89_RIGHT\t30\nnCoV-2019_90_LEFT\t28\nnCoV-2019_90_RIGHT\t21\nnCoV-2019_91_LEFT\t27\nnCoV-2019_91_RIGHT\t2\nnCoV-2019_92_LEFT\t9\nnCoV-2019_92_RIGHT\t14\nnCoV-2019_93_LEFT\t38\nnCoV-2019_93_RIGHT\t23\nnCoV-2019_94_LEFT\t116\nnCoV-2019_94_RIGHT\t55\nnCoV-2019_95_LEFT\t39\nnCoV-2019_95_RIGHT\t8\nnCoV-2019_96_LEFT\t24\nnCoV-2019_96_RIGHT\t17\nnCoV-2019_97_LEFT\t0\nnCoV-2019_97_RIGHT\t1\nnCoV-2019_98_LEFT\t2\nnCoV-2019_98_RIGHT\t2\n\nTrimmed primers from 13.29% (6871) of reads.\n3.5% (1811) of reads were quality trimmed below the minimum length of 30 bp and were not written to file.\n84.15% (43493) of reads started outside of primer regions. Since the -e flag was given, these reads were written to file.\n58.16% (30061) of reads had their insert size smaller than their read length\n[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:45:18", "plugin": "core", "name": "end_epoch", "raw_value": "1727293518.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:45:17", "plugin": "core", "name": "start_epoch", "raw_value": "1727293517.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "ivar_trim/1.4.3+galaxy0-1", "has_data": true, "data": {"tool_id": "ivar_trim", "tool_version": "1.4.3+galaxy0", "test_index": 1, "time_seconds": 57.418792724609375, "inputs": {"input_bam": {"src": "hda", "id": "8e9199d6b3c08534"}, "primer|input_bed": {"src": "hda", "id": "7bd77aeaded37e73"}, "inc_primers": true, "trimmed_length|min_len": "30", "trimmed_length|filter": "custom"}, "job": {"model_class": "Job", "id": "f9fdf8e84e663c13", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:46:00.604881", "update_time": "2024-09-25T19:46:31.208949", "galaxy_version": "24.1", "external_id": "gxy-pnfs4", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/4/d/b/dataset_4dbd8c2d-0285-4fa1-a84e-507ac7d7116a.dat' bed.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/a250929be21b/ivar_trim/sanitize_bed.py' bed.bed && ln -s '/galaxy/server/database/objects/8/1/2/dataset_812bd9c4-ab1e-47e6-a346-eca7a31e3721.dat' sorted.bam && ln -s '/galaxy/server/database/objects/_metadata_files/4/b/0/metadata_4b02042f-0980-4363-ae66-247e29474312.dat' sorted.bam.bai && ivar trim -i sorted.bam -b bed.bed -x 0 -e -m 30 -q 20 -s 4 | samtools sort -@ ${GALAXY_SLOTS:-1} -T \"${TMPDIR:-.}\" -o trimmed.sorted.bam -", "user_email": "tests@fake.org", "command_version": "iVar version 1.4.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "trimmed_length": "{\"__current_case__\": 2, \"filter\": \"custom\", \"min_len\": \"30\"}", "window_width": "\"4\"", "min_qual": "\"20\"", "inc_primers": "true", "primer_pos_wiggle": "\"0\"", "amplicons": "{\"__current_case__\": 2, \"filter_by\": \"\"}", "primer": "{\"__current_case__\": 0, \"input_bed\": {\"values\": [{\"id\": 292, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"input_bam": {"id": "8e9199d6b3c08534", "src": "hda", "uuid": "812bd9c4-ab1e-47e6-a346-eca7a31e3721"}, "primer|input_bed": {"id": "156022329fed2b5c", "src": "hda", "uuid": "4dbd8c2d-0285-4fa1-a84e-507ac7d7116a"}}, "outputs": {"output_bam": {"id": "933cf60f90606c40", "src": "hda", "uuid": "a2393304-faa1-4353-82ac-4cc4f01d8685"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Found 196 primers in BED file\nReading from sorted.bam\n\n-------\nResults: \nPrimer Name\tRead Count\nregion_0\t25\nregion_1\t9\nregion_2\t10\nregion_3\t17\nregion_4\t22\nregion_5\t29\nregion_6\t20\nregion_7\t5\nregion_8\t4\nregion_9\t16\nregion_10\t17\nregion_11\t10\nregion_12\t21\nregion_13\t14\nregion_14\t5\nregion_15\t10\nregion_16\t18\nregion_17\t11\nregion_18\t20\nregion_19\t11\nregion_20\t15\nregion_21\t31\nregion_22\t48\nregion_23\t11\nregion_24\t31\nregion_25\t64\nregion_26\t53\nregion_27\t89\nregion_28\t64\nregion_29\t57\nregion_30\t168\nregion_31\t112\nregion_32\t100\nregion_33\t23\nregion_34\t19\nregion_35\t42\nregion_36\t72\nregion_37\t43\nregion_38\t31\nregion_39\t63\nregion_40\t126\nregion_41\t23\nregion_42\t55\nregion_43\t58\nregion_44\t46\nregion_45\t2\nregion_46\t22\nregion_47\t6\nregion_48\t7\nregion_49\t11\nregion_50\t13\nregion_51\t14\nregion_52\t70\nregion_53\t31\nregion_54\t15\nregion_55\t6\nregion_56\t4\nregion_57\t70\nregion_58\t10\nregion_59\t26\nregion_60\t33\nregion_61\t75\nregion_62\t119\nregion_63\t52\nregion_64\t23\nregion_65\t43\nregion_66\t51\nregion_67\t40\nregion_68\t44\nregion_69\t86\nregion_70\t113\nregion_71\t131\nregion_72\t74\nregion_73\t163\nregion_74\t185\nregion_75\t113\nregion_76\t97\nregion_77\t39\nregion_78\t67\nregion_79\t17\nregion_80\t31\nregion_81\t5\nregion_82\t39\nregion_83\t89\nregion_84\t47\nregion_85\t23\nregion_86\t51\nregion_87\t70\nregion_88\t43\nregion_89\t16\nregion_90\t11\nregion_91\t35\nregion_92\t27\nregion_93\t25\nregion_94\t74\nregion_95\t41\nregion_96\t40\nregion_97\t54\nregion_98\t26\nregion_99\t19\nregion_100\t81\nregion_101\t47\nregion_102\t33\nregion_103\t28\nregion_104\t75\nregion_105\t35\nregion_106\t44\nregion_107\t13\nregion_108\t66\nregion_109\t96\nregion_110\t35\nregion_111\t69\nregion_112\t112\nregion_113\t78\nregion_114\t15\nregion_115\t6\nregion_116\t35\nregion_117\t23\nregion_118\t22\nregion_119\t19\nregion_120\t33\nregion_121\t33\nregion_122\t16\nregion_123\t17\nregion_124\t47\nregion_125\t31\nregion_126\t6\nregion_127\t8\nregion_128\t6\nregion_129\t59\nregion_130\t29\nregion_131\t2\nregion_132\t6\nregion_133\t0\nregion_134\t8\nregion_135\t9\nregion_136\t17\nregion_137\t5\nregion_138\t0\nregion_139\t1\nregion_140\t1\nregion_141\t5\nregion_142\t7\nregion_143\t4\nregion_144\t0\nregion_145\t4\nregion_146\t0\nregion_147\t0\nregion_148\t2\nregion_149\t1\nregion_150\t2\nregion_151\t13\nregion_152\t27\nregion_153\t87\nregion_154\t63\nregion_155\t23\nregion_156\t5\nregion_157\t17\nregion_158\t92\nregion_159\t33\nregion_160\t28\nregion_161\t79\nregion_162\t150\nregion_163\t50\nregion_164\t22\nregion_165\t41\nregion_166\t32\nregion_167\t50\nregion_168\t77\nregion_169\t37\nregion_170\t54\nregion_171\t30\nregion_172\t48\nregion_173\t3\nregion_174\t58\nregion_175\t91\nregion_176\t37\nregion_177\t30\nregion_178\t28\nregion_179\t21\nregion_180\t27\nregion_181\t2\nregion_182\t9\nregion_183\t14\nregion_184\t38\nregion_185\t23\nregion_186\t116\nregion_187\t55\nregion_188\t39\nregion_189\t8\nregion_190\t24\nregion_191\t17\nregion_192\t0\nregion_193\t1\nregion_194\t2\nregion_195\t2\n\nTrimmed primers from 13.29% (6871) of reads.\n3.5% (1811) of reads were quality trimmed below the minimum length of 30 bp and were not written to file.\n84.15% (43493) of reads started outside of primer regions. Since the -e flag was given, these reads were written to file.\n58.16% (30061) of reads had their insert size smaller than their read length\n[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Found 196 primers in BED file\nReading from sorted.bam\n\n-------\nResults: \nPrimer Name\tRead Count\nregion_0\t25\nregion_1\t9\nregion_2\t10\nregion_3\t17\nregion_4\t22\nregion_5\t29\nregion_6\t20\nregion_7\t5\nregion_8\t4\nregion_9\t16\nregion_10\t17\nregion_11\t10\nregion_12\t21\nregion_13\t14\nregion_14\t5\nregion_15\t10\nregion_16\t18\nregion_17\t11\nregion_18\t20\nregion_19\t11\nregion_20\t15\nregion_21\t31\nregion_22\t48\nregion_23\t11\nregion_24\t31\nregion_25\t64\nregion_26\t53\nregion_27\t89\nregion_28\t64\nregion_29\t57\nregion_30\t168\nregion_31\t112\nregion_32\t100\nregion_33\t23\nregion_34\t19\nregion_35\t42\nregion_36\t72\nregion_37\t43\nregion_38\t31\nregion_39\t63\nregion_40\t126\nregion_41\t23\nregion_42\t55\nregion_43\t58\nregion_44\t46\nregion_45\t2\nregion_46\t22\nregion_47\t6\nregion_48\t7\nregion_49\t11\nregion_50\t13\nregion_51\t14\nregion_52\t70\nregion_53\t31\nregion_54\t15\nregion_55\t6\nregion_56\t4\nregion_57\t70\nregion_58\t10\nregion_59\t26\nregion_60\t33\nregion_61\t75\nregion_62\t119\nregion_63\t52\nregion_64\t23\nregion_65\t43\nregion_66\t51\nregion_67\t40\nregion_68\t44\nregion_69\t86\nregion_70\t113\nregion_71\t131\nregion_72\t74\nregion_73\t163\nregion_74\t185\nregion_75\t113\nregion_76\t97\nregion_77\t39\nregion_78\t67\nregion_79\t17\nregion_80\t31\nregion_81\t5\nregion_82\t39\nregion_83\t89\nregion_84\t47\nregion_85\t23\nregion_86\t51\nregion_87\t70\nregion_88\t43\nregion_89\t16\nregion_90\t11\nregion_91\t35\nregion_92\t27\nregion_93\t25\nregion_94\t74\nregion_95\t41\nregion_96\t40\nregion_97\t54\nregion_98\t26\nregion_99\t19\nregion_100\t81\nregion_101\t47\nregion_102\t33\nregion_103\t28\nregion_104\t75\nregion_105\t35\nregion_106\t44\nregion_107\t13\nregion_108\t66\nregion_109\t96\nregion_110\t35\nregion_111\t69\nregion_112\t112\nregion_113\t78\nregion_114\t15\nregion_115\t6\nregion_116\t35\nregion_117\t23\nregion_118\t22\nregion_119\t19\nregion_120\t33\nregion_121\t33\nregion_122\t16\nregion_123\t17\nregion_124\t47\nregion_125\t31\nregion_126\t6\nregion_127\t8\nregion_128\t6\nregion_129\t59\nregion_130\t29\nregion_131\t2\nregion_132\t6\nregion_133\t0\nregion_134\t8\nregion_135\t9\nregion_136\t17\nregion_137\t5\nregion_138\t0\nregion_139\t1\nregion_140\t1\nregion_141\t5\nregion_142\t7\nregion_143\t4\nregion_144\t0\nregion_145\t4\nregion_146\t0\nregion_147\t0\nregion_148\t2\nregion_149\t1\nregion_150\t2\nregion_151\t13\nregion_152\t27\nregion_153\t87\nregion_154\t63\nregion_155\t23\nregion_156\t5\nregion_157\t17\nregion_158\t92\nregion_159\t33\nregion_160\t28\nregion_161\t79\nregion_162\t150\nregion_163\t50\nregion_164\t22\nregion_165\t41\nregion_166\t32\nregion_167\t50\nregion_168\t77\nregion_169\t37\nregion_170\t54\nregion_171\t30\nregion_172\t48\nregion_173\t3\nregion_174\t58\nregion_175\t91\nregion_176\t37\nregion_177\t30\nregion_178\t28\nregion_179\t21\nregion_180\t27\nregion_181\t2\nregion_182\t9\nregion_183\t14\nregion_184\t38\nregion_185\t23\nregion_186\t116\nregion_187\t55\nregion_188\t39\nregion_189\t8\nregion_190\t24\nregion_191\t17\nregion_192\t0\nregion_193\t1\nregion_194\t2\nregion_195\t2\n\nTrimmed primers from 13.29% (6871) of reads.\n3.5% (1811) of reads were quality trimmed below the minimum length of 30 bp and were not written to file.\n84.15% (43493) of reads started outside of primer regions. Since the -e flag was given, these reads were written to file.\n58.16% (30061) of reads had their insert size smaller than their read length\n[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-25 19:46:17", "plugin": "core", "name": "end_epoch", "raw_value": "1727293577.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:46:17", "plugin": "core", "name": "start_epoch", "raw_value": "1727293577.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "ivar_trim/1.4.3+galaxy0-2", "has_data": true, "data": {"tool_id": "ivar_trim", "tool_version": "1.4.3+galaxy0", "test_index": 2, "time_seconds": 41.5969557762146, "inputs": {"input_bam": {"src": "hda", "id": "a150afbcfe1d9858"}, "primer|input_bed": {"src": "hda", "id": "b968611f7cdf853d"}, "primer|source": "history", "trimmed_length|min_len": "30", "trimmed_length|filter": "custom"}, "job": {"model_class": "Job", "id": "8badc81ffac91a55", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:46:56.375415", "update_time": "2024-09-25T19:47:12.936400", "galaxy_version": "24.1", "external_id": "gxy-zddvg", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/7/3/6/dataset_7364eafe-1cac-494f-9491-76db50a8b8fc.dat' bed.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/a250929be21b/ivar_trim/sanitize_bed.py' bed.bed && ln -s '/galaxy/server/database/objects/4/0/b/dataset_40b5b0f3-bbbd-410e-9a35-f10ed5fe1249.dat' sorted.bam && ln -s '/galaxy/server/database/objects/_metadata_files/c/b/1/metadata_cb1b9ae6-0469-4825-89cd-e86535fd5b13.dat' sorted.bam.bai && ivar trim -i sorted.bam -b bed.bed -x 0 -m 30 -q 20 -s 4 | samtools sort -@ ${GALAXY_SLOTS:-1} -T \"${TMPDIR:-.}\" -o trimmed.sorted.bam -", "user_email": "tests@fake.org", "command_version": "iVar version 1.4.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "trimmed_length": "{\"__current_case__\": 2, \"filter\": \"custom\", \"min_len\": \"30\"}", "window_width": "\"4\"", "min_qual": "\"20\"", "inc_primers": "false", "primer_pos_wiggle": "\"0\"", "amplicons": "{\"__current_case__\": 2, \"filter_by\": \"\"}", "primer": "{\"__current_case__\": 0, \"input_bed\": {\"values\": [{\"id\": 295, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"input_bam": {"id": "a150afbcfe1d9858", "src": "hda", "uuid": "40b5b0f3-bbbd-410e-9a35-f10ed5fe1249"}, "primer|input_bed": {"id": "b968611f7cdf853d", "src": "hda", "uuid": "7364eafe-1cac-494f-9491-76db50a8b8fc"}}, "outputs": {"output_bam": {"id": "08cd75d6d17d51f6", "src": "hda", "uuid": "f561b60e-0100-4e9b-8443-8a8aaa5069f4"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Found 68 primers in BED file\nReading from sorted.bam\n\n-------\nResults: \nPrimer Name\tRead Count\n400_1_out_R\t116\n400_2_out_L\t265\n400_2_out_R\t269\n400_3_out_L*\t47\n400_3_out_R*\t55\n400_4_out_L\t123\n400_4_out_R\t123\n400_5_out_L\t1083\n400_5_out_R\t1044\n400_6_out_L\t139\n400_6_out_R\t140\n400_7_out_L\t246\n400_7_out_R\t251\n400_8_out_L*\t164\n400_8_out_R*\t164\n400_9_out_L*\t105\n400_9_out_R*\t104\n400_10_out_L\t358\n400_10_out_R\t358\n400_11_out_L\t1538\n400_11_out_R\t1541\n400_12_out_L\t297\n400_12_out_R\t293\n400_13_out_L\t209\n400_13_out_R\t229\n400_14_out_L*\t736\n400_14_out_R*\t735\n400_15_out_L\t87\n400_15_out_R\t82\n400_16_out_L*\t498\n400_16_out_R*\t493\n400_17_out_L**\t1420\n400_17_out_R**\t1415\n400_18_out_L**\t9\n400_18_out_R**\t9\n400_19_out_L\t43\n400_19_out_R\t50\n400_20_out_L*\t2128\n400_20_out_R*\t2158\n400_21_out_L*\t18\n400_21_out_R*\t10\n400_22_out_L**\t33\n400_22_out_R**\t5\n400_23_out_L\t179\n400_23_out_R\t169\n400_24_out_L**\t80\n400_24_out_R**\t80\n400_25_out_L**\t3035\n400_25_out_R**\t3073\n400_26_out_L\t423\n400_26_out_R\t428\n400_27_out_L\t104\n400_27_out_R\t6\n400_28_out_L\t41\n400_28_out_R\t43\n400_29_out_L\t113\n400_29_out_R\t118\n400_30_out_L\t1057\n400_30_out_R\t1054\n400_31_out_L\t166\n400_31_out_R\t170\n400_32_out_L\t280\n400_32_out_R\t283\n400_33_out_L*\t436\n400_33_out_R*\t433\n400_34_out_L*\t688\n400_34_out_R*\t688\n400_35_out_L\t0\n\nTrimmed primers from 99.24% (32302) of reads.\n10.73% (3493) of reads were quality trimmed below the minimum length of 30 bp and were not written to file.\n0.65% (212) of reads that started outside of primer regions were not written to file\n0.91% (296) of reads had their insert size smaller than their read length\n[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Found 68 primers in BED file\nReading from sorted.bam\n\n-------\nResults: \nPrimer Name\tRead Count\n400_1_out_R\t116\n400_2_out_L\t265\n400_2_out_R\t269\n400_3_out_L*\t47\n400_3_out_R*\t55\n400_4_out_L\t123\n400_4_out_R\t123\n400_5_out_L\t1083\n400_5_out_R\t1044\n400_6_out_L\t139\n400_6_out_R\t140\n400_7_out_L\t246\n400_7_out_R\t251\n400_8_out_L*\t164\n400_8_out_R*\t164\n400_9_out_L*\t105\n400_9_out_R*\t104\n400_10_out_L\t358\n400_10_out_R\t358\n400_11_out_L\t1538\n400_11_out_R\t1541\n400_12_out_L\t297\n400_12_out_R\t293\n400_13_out_L\t209\n400_13_out_R\t229\n400_14_out_L*\t736\n400_14_out_R*\t735\n400_15_out_L\t87\n400_15_out_R\t82\n400_16_out_L*\t498\n400_16_out_R*\t493\n400_17_out_L**\t1420\n400_17_out_R**\t1415\n400_18_out_L**\t9\n400_18_out_R**\t9\n400_19_out_L\t43\n400_19_out_R\t50\n400_20_out_L*\t2128\n400_20_out_R*\t2158\n400_21_out_L*\t18\n400_21_out_R*\t10\n400_22_out_L**\t33\n400_22_out_R**\t5\n400_23_out_L\t179\n400_23_out_R\t169\n400_24_out_L**\t80\n400_24_out_R**\t80\n400_25_out_L**\t3035\n400_25_out_R**\t3073\n400_26_out_L\t423\n400_26_out_R\t428\n400_27_out_L\t104\n400_27_out_R\t6\n400_28_out_L\t41\n400_28_out_R\t43\n400_29_out_L\t113\n400_29_out_R\t118\n400_30_out_L\t1057\n400_30_out_R\t1054\n400_31_out_L\t166\n400_31_out_R\t170\n400_32_out_L\t280\n400_32_out_R\t283\n400_33_out_L*\t436\n400_33_out_R*\t433\n400_34_out_L*\t688\n400_34_out_R*\t688\n400_35_out_L\t0\n\nTrimmed primers from 99.24% (32302) of reads.\n10.73% (3493) of reads were quality trimmed below the minimum length of 30 bp and were not written to file.\n0.65% (212) of reads that started outside of primer regions were not written to file\n0.91% (296) of reads had their insert size smaller than their read length\n[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-25 19:46:58", "plugin": "core", "name": "end_epoch", "raw_value": "1727293618.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:46:58", "plugin": "core", "name": "start_epoch", "raw_value": "1727293618.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "ivar_trim/1.4.3+galaxy0-3", "has_data": true, "data": {"tool_id": "ivar_trim", "tool_version": "1.4.3+galaxy0", "test_index": 3, "time_seconds": 42.440638065338135, "inputs": {"input_bam": {"src": "hda", "id": "fadc93571e71f0ad"}, "primer|input_bed": {"src": "hda", "id": "4fa9117d38c05cdf"}, "primer|source": "history", "trimmed_length|filter": "auto"}, "job": {"model_class": "Job", "id": "407b8f0da0822d99", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:47:39.626305", "update_time": "2024-09-25T19:47:55.512161", "galaxy_version": "24.1", "external_id": "gxy-2x2lj", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/5/c/d/dataset_5cd55746-4aa8-4833-bdbb-f532a509390a.dat' bed.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/a250929be21b/ivar_trim/sanitize_bed.py' bed.bed && ln -s '/galaxy/server/database/objects/c/8/1/dataset_c812b221-0dfa-4645-9f21-8f733533270c.dat' sorted.bam && ln -s '/galaxy/server/database/objects/_metadata_files/1/2/d/metadata_12d1f08c-300b-4e8b-987d-3d30efae6232.dat' sorted.bam.bai && ivar trim -i sorted.bam -b bed.bed -x 0 -m -1 -q 20 -s 4 | samtools sort -@ ${GALAXY_SLOTS:-1} -T \"${TMPDIR:-.}\" -o trimmed.sorted.bam -", "user_email": "tests@fake.org", "command_version": "iVar version 1.4.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "trimmed_length": "{\"__current_case__\": 1, \"filter\": \"auto\"}", "window_width": "\"4\"", "min_qual": "\"20\"", "inc_primers": "false", "primer_pos_wiggle": "\"0\"", "amplicons": "{\"__current_case__\": 2, \"filter_by\": \"\"}", "primer": "{\"__current_case__\": 0, \"input_bed\": {\"values\": [{\"id\": 298, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"input_bam": {"id": "fadc93571e71f0ad", "src": "hda", "uuid": "c812b221-0dfa-4645-9f21-8f733533270c"}, "primer|input_bed": {"id": "4fa9117d38c05cdf", "src": "hda", "uuid": "5cd55746-4aa8-4833-bdbb-f532a509390a"}}, "outputs": {"output_bam": {"id": "a11de70be7ac56fe", "src": "hda", "uuid": "68113c9f-4298-44fa-811a-2fbb8adbacb4"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Found 68 primers in BED file\nReading from sorted.bam\nMinimum Read Length based on 1000 reads: 125\n\n-------\nResults: \nPrimer Name\tRead Count\n400_1_out_R\t156\n400_2_out_L\t227\n400_2_out_R\t238\n400_3_out_L*\t76\n400_3_out_R*\t76\n400_4_out_L\t91\n400_4_out_R\t98\n400_5_out_L\t1548\n400_5_out_R\t1541\n400_6_out_L\t37\n400_6_out_R\t38\n400_7_out_L\t540\n400_7_out_R\t538\n400_8_out_L*\t143\n400_8_out_R*\t143\n400_9_out_L*\t90\n400_9_out_R*\t93\n400_10_out_L\t400\n400_10_out_R\t402\n400_11_out_L\t2536\n400_11_out_R\t2534\n400_12_out_L\t146\n400_12_out_R\t141\n400_13_out_L\t299\n400_13_out_R\t307\n400_14_out_L*\t676\n400_14_out_R*\t671\n400_15_out_L\t183\n400_15_out_R\t180\n400_16_out_L*\t419\n400_16_out_R*\t417\n400_17_out_L**\t2322\n400_17_out_R**\t2315\n400_18_out_L**\t32\n400_18_out_R**\t6\n400_19_out_L\t67\n400_19_out_R\t69\n400_20_out_L*\t1653\n400_20_out_R*\t1681\n400_21_out_L*\t18\n400_21_out_R*\t13\n400_22_out_L**\t18\n400_22_out_R**\t2\n400_23_out_L\t297\n400_23_out_R\t292\n400_24_out_L**\t61\n400_24_out_R**\t68\n400_25_out_L**\t4363\n400_25_out_R**\t4382\n400_26_out_L\t310\n400_26_out_R\t305\n400_27_out_L\t95\n400_27_out_R\t21\n400_28_out_L\t17\n400_28_out_R\t17\n400_29_out_L\t185\n400_29_out_R\t187\n400_30_out_L\t1512\n400_30_out_R\t1510\n400_31_out_L\t266\n400_31_out_R\t273\n400_32_out_L\t413\n400_32_out_R\t411\n400_33_out_L*\t546\n400_33_out_R*\t536\n400_34_out_L*\t699\n400_34_out_R*\t699\n400_35_out_L\t0\n\nTrimmed primers from 99.17% (40620) of reads.\n18.42% (7545) of reads were quality trimmed below the minimum length of 125 bp and were not written to file.\n0.67% (274) of reads that started outside of primer regions were not written to file\n0.57% (232) of reads had their insert size smaller than their read length\n[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Found 68 primers in BED file\nReading from sorted.bam\nMinimum Read Length based on 1000 reads: 125\n\n-------\nResults: \nPrimer Name\tRead Count\n400_1_out_R\t156\n400_2_out_L\t227\n400_2_out_R\t238\n400_3_out_L*\t76\n400_3_out_R*\t76\n400_4_out_L\t91\n400_4_out_R\t98\n400_5_out_L\t1548\n400_5_out_R\t1541\n400_6_out_L\t37\n400_6_out_R\t38\n400_7_out_L\t540\n400_7_out_R\t538\n400_8_out_L*\t143\n400_8_out_R*\t143\n400_9_out_L*\t90\n400_9_out_R*\t93\n400_10_out_L\t400\n400_10_out_R\t402\n400_11_out_L\t2536\n400_11_out_R\t2534\n400_12_out_L\t146\n400_12_out_R\t141\n400_13_out_L\t299\n400_13_out_R\t307\n400_14_out_L*\t676\n400_14_out_R*\t671\n400_15_out_L\t183\n400_15_out_R\t180\n400_16_out_L*\t419\n400_16_out_R*\t417\n400_17_out_L**\t2322\n400_17_out_R**\t2315\n400_18_out_L**\t32\n400_18_out_R**\t6\n400_19_out_L\t67\n400_19_out_R\t69\n400_20_out_L*\t1653\n400_20_out_R*\t1681\n400_21_out_L*\t18\n400_21_out_R*\t13\n400_22_out_L**\t18\n400_22_out_R**\t2\n400_23_out_L\t297\n400_23_out_R\t292\n400_24_out_L**\t61\n400_24_out_R**\t68\n400_25_out_L**\t4363\n400_25_out_R**\t4382\n400_26_out_L\t310\n400_26_out_R\t305\n400_27_out_L\t95\n400_27_out_R\t21\n400_28_out_L\t17\n400_28_out_R\t17\n400_29_out_L\t185\n400_29_out_R\t187\n400_30_out_L\t1512\n400_30_out_R\t1510\n400_31_out_L\t266\n400_31_out_R\t273\n400_32_out_L\t413\n400_32_out_R\t411\n400_33_out_L*\t546\n400_33_out_R*\t536\n400_34_out_L*\t699\n400_34_out_R*\t699\n400_35_out_L\t0\n\nTrimmed primers from 99.17% (40620) of reads.\n18.42% (7545) of reads were quality trimmed below the minimum length of 125 bp and were not written to file.\n0.67% (274) of reads that started outside of primer regions were not written to file\n0.57% (232) of reads had their insert size smaller than their read length\n[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:47:42", "plugin": "core", "name": "end_epoch", "raw_value": "1727293662.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:47:41", "plugin": "core", "name": "start_epoch", "raw_value": "1727293661.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "ivar_trim/1.4.3+galaxy0-4", "has_data": true, "data": {"tool_id": "ivar_trim", "tool_version": "1.4.3+galaxy0", "test_index": 4, "status": "skip"}}, {"id": "ivar_trim/1.4.3+galaxy0-5", "has_data": true, "data": {"tool_id": "ivar_trim", "tool_version": "1.4.3+galaxy0", "test_index": 5, "status": "skip"}}, {"id": "limma_voom/3.58.1+galaxy0-0", "has_data": true, "data": {"tool_id": "limma_voom", "tool_version": "3.58.1+galaxy0", "test_index": 0, "time_seconds": 96.4143500328064, "inputs": {"input|counts": {"src": "hda", "id": "c142bf99114a19bc"}, "input|fact|rep_factor_0|factorName": "Genotype", "input|fact|rep_factor_0|groupNames": "Mut,Mut,Mut,WT,WT,WT", "input|format": "matrix", "cont|rep_contrast_0|contrast": "Mut-WT", "cont|rep_contrast_1|contrast": "WT-Mut", "cont|cfile": "no", "adv|topgenes": "6", "adv|normalisationOption": "TMM"}, "job": {"model_class": "Job", "id": "0076c240c1215f91", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T18:42:14.573054", "update_time": "2024-09-25T18:43:27.315194", "galaxy_version": "24.1", "external_id": "gxy-bzzzg", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/6/d/7/dataset_6d799cdf-badb-40aa-8e2f-a13abbecbda0.dat' -o '/galaxy/server/database/objects/6/d/7/dataset_6d799cdf-badb-40aa-8e2f-a13abbecbda0_files' -m '/galaxy/server/database/objects/5/8/e/dataset_58e5b857-afd6-465d-8170-5148b6bb2c3f.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -D 'Mut-WT,WT-Mut' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/6/d/7/dataset_6d799cdf-badb-40aa-8e2f-a13abbecbda0_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/6/d/7/dataset_6d799cdf-badb-40aa-8e2f-a13abbecbda0_files'", "user_email": "tests@fake.org", "command_version": "R version 4.3.2 (2023-10-31) -- \"Eye Holes\", limma version 3.58.1, edgeR version 4.0.2, statmod version 1.5.0, scales version 1.3.0, rjson version 0.2.21, getopt version 1.20.4, gplots version 3.1.3.1, Glimma version 2.12.0", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"lfc\": \"0.0\", \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true, \"topgenes\": \"6\", \"treat\": false}", "out": "{\"filtCounts\": false, \"libinfo\": false, \"normCounts\": false, \"plots\": \"i\", \"rdaOption\": false, \"rscript\": false}", "f": "{\"filt\": {\"__current_case__\": 1, \"filt_select\": \"no\"}}", "cont": "{\"__current_case__\": 1, \"cfile\": \"no\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": \"Mut-WT\"}, {\"__index__\": 1, \"contrast\": \"WT-Mut\"}]}", "anno": "{\"__current_case__\": 1, \"annoOpt\": \"no\"}", "input": "{\"__current_case__\": 1, \"counts\": {\"values\": [{\"id\": 44, \"src\": \"hda\"}]}, \"fact\": {\"__current_case__\": 1, \"ffile\": \"no\", \"rep_factor\": [{\"__index__\": 0, \"factorName\": \"Genotype\", \"groupNames\": \"Mut,Mut,Mut,WT,WT,WT\"}]}, \"format\": \"matrix\"}", "deMethod": "{\"__current_case__\": 0, \"de_select\": \"voom\", \"weightOption\": false}"}, "inputs": {"input|counts": {"id": "c142bf99114a19bc", "src": "hda", "uuid": "58e5b857-afd6-465d-8170-5148b6bb2c3f"}}, "outputs": {"outReport": {"id": "9e014b855bf11704", "src": "hda", "uuid": "6d799cdf-badb-40aa-8e2f-a13abbecbda0"}, "__new_primary_file_outTables|limma-voom_Mut-WT__": {"id": "fc4ebd8775159ed3", "src": "hda", "uuid": "9247a5c5-27fe-48dd-89aa-a1aca7e2105b"}, "__new_primary_file_outTables|limma-voom_WT-Mut__": {"id": "8a8d7a47f4b0f907", "src": "hda", "uuid": "6873cf20-2de1-4561-8ef3-7aec80b19e1c"}}, "copied_from_job_id": null, "output_collections": {"outTables": {"src": "hdca", "id": "beda644706419afa"}}, "tool_stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_stdout": "", "job_stderr": "", "stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:42:44", "plugin": "core", "name": "start_epoch", "raw_value": "1727289764.0000000"}, {"title": "Job End Time", "value": "2024-09-25 18:43:08", "plugin": "core", "name": "end_epoch", "raw_value": "1727289788.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "24 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "24.0000000"}]}, "status": "success"}}, {"id": "limma_voom/3.58.1+galaxy0-0", "has_data": true, "data": {"tool_id": "limma_voom", "tool_version": "3.58.1+galaxy0", "test_index": 0, "time_seconds": 60.87278389930725, "inputs": {"input|counts": {"src": "hda", "id": "075aef97948ba53a"}, "input|fact|rep_factor_0|factorName": "Genotype", "input|fact|rep_factor_0|groupNames": "Mut,Mut,Mut,WT,WT,WT", "input|format": "matrix", "cont|rep_contrast_0|contrast": "Mut-WT", "cont|rep_contrast_1|contrast": "WT-Mut", "cont|cfile": "no", "adv|topgenes": "6", "adv|normalisationOption": "TMM"}, "job": {"model_class": "Job", "id": "122ebe4b5e90dd59", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.58.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T18:52:28.439756", "update_time": "2024-09-25T18:53:06.707443", "galaxy_version": "24.1", "external_id": "gxy-d47v2", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/4/e/5/dataset_4e559693-c849-4f26-bddd-12f0cf06484f.dat' -o '/galaxy/server/database/objects/4/e/5/dataset_4e559693-c849-4f26-bddd-12f0cf06484f_files' -m '/galaxy/server/database/objects/7/2/a/dataset_72a212c5-3103-4a30-8140-4b98589bcf0a.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -D 'Mut-WT,WT-Mut' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/4/e/5/dataset_4e559693-c849-4f26-bddd-12f0cf06484f_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/4/e/5/dataset_4e559693-c849-4f26-bddd-12f0cf06484f_files'", "user_email": "tests@fake.org", "command_version": "R version 4.3.2 (2023-10-31) -- \"Eye Holes\", limma version 3.58.1, edgeR version 4.0.2, statmod version 1.5.0, scales version 1.3.0, rjson version 0.2.21, getopt version 1.20.4, gplots version 3.1.3.1, Glimma version 2.12.0", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"lfc\": \"0.0\", \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true, \"topgenes\": \"6\", \"treat\": false}", "out": "{\"filtCounts\": false, \"libinfo\": false, \"normCounts\": false, \"plots\": \"i\", \"rdaOption\": false, \"rscript\": false}", "f": "{\"filt\": {\"__current_case__\": 1, \"filt_select\": \"no\"}}", "cont": "{\"__current_case__\": 1, \"cfile\": \"no\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": \"Mut-WT\"}, {\"__index__\": 1, \"contrast\": \"WT-Mut\"}]}", "anno": "{\"__current_case__\": 1, \"annoOpt\": \"no\"}", "input": "{\"__current_case__\": 1, \"counts\": {\"values\": [{\"id\": 93, \"src\": \"hda\"}]}, \"fact\": {\"__current_case__\": 1, \"ffile\": \"no\", \"rep_factor\": [{\"__index__\": 0, \"factorName\": \"Genotype\", \"groupNames\": \"Mut,Mut,Mut,WT,WT,WT\"}]}, \"format\": \"matrix\"}", "deMethod": "{\"__current_case__\": 0, \"de_select\": \"voom\", \"weightOption\": false}"}, "inputs": {"input|counts": {"id": "075aef97948ba53a", "src": "hda", "uuid": "72a212c5-3103-4a30-8140-4b98589bcf0a"}}, "outputs": {"outReport": {"id": "875455ec67c7df27", "src": "hda", "uuid": "4e559693-c849-4f26-bddd-12f0cf06484f"}, "__new_primary_file_outTables|limma-voom_Mut-WT__": {"id": "d862bd0c6ee480d6", "src": "hda", "uuid": "66ae3a5c-2803-4dcf-9809-0ea8d4029f84"}, "__new_primary_file_outTables|limma-voom_WT-Mut__": {"id": "c4161aec13e7ea95", "src": "hda", "uuid": "f3093c33-66ae-4ed4-9aa1-e1506e5f62ac"}}, "copied_from_job_id": null, "output_collections": {"outTables": {"src": "hdca", "id": "94da987fbf0a05eb"}}, "tool_stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_stdout": "", "job_stderr": "", "stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_messages": [], 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{\"__current_case__\": 1, \"ffile\": \"no\", \"rep_factor\": [{\"__index__\": 0, \"factorName\": \"Genotype\", \"groupNames\": \"Mut,Mut,Mut,WT,WT,WT\"}]}, \"format\": \"matrix\"}", "deMethod": "{\"__current_case__\": 0, \"de_select\": \"voom\", \"weightOption\": false}"}, "inputs": {"input|counts": {"id": "2adc1e2ae6a5c037", "src": "hda", "uuid": "1abad90b-33f9-49da-84f6-a5e9cfb251e3"}, "anno|geneanno": {"id": "cbb50fced67ac6b8", "src": "hda", "uuid": "23ea18a0-b6d0-48d4-ae34-0d42a75bc66a"}}, "outputs": {"outReport": {"id": "08b9404136c76ef6", "src": "hda", "uuid": "429af1e6-336c-4f68-9903-f649a31f2e83"}, "__new_primary_file_outTables|limma-voom_Mut-WT__": {"id": "8847fe294eeebc88", "src": "hda", "uuid": "819edb0d-f29d-4838-af7e-ea6054c657db"}}, "copied_from_job_id": null, "output_collections": {"outTables": {"src": "hdca", "id": "c99a2d897e0b2e76"}}, "tool_stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_stdout": "", "job_stderr": "", "stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "25 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "25.0000000"}, {"title": "Job End Time", "value": "2024-09-25 18:53:56", "plugin": "core", "name": "end_epoch", "raw_value": "1727290436.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:53:31", "plugin": "core", "name": "start_epoch", "raw_value": "1727290411.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "limma_voom/3.58.1+galaxy0-10", "has_data": true, "data": {"tool_id": "limma_voom", "tool_version": "3.58.1+galaxy0", "test_index": 10, "time_seconds": 12.31203556060791, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: 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'/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/d/e/9/dataset_de9e0b58-ed6e-4db6-b47f-bfc2591780be.dat' -o '/galaxy/server/database/objects/d/e/9/dataset_de9e0b58-ed6e-4db6-b47f-bfc2591780be_files' -m '/galaxy/server/database/objects/d/a/8/dataset_da8e21b9-6da7-4c65-88a6-f0da2c0820c7.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -C '/galaxy/server/database/objects/0/1/8/dataset_0183e8a8-8586-499d-b9c1-e3e34ab54eaa.dat' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/d/e/9/dataset_de9e0b58-ed6e-4db6-b47f-bfc2591780be_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/d/e/9/dataset_de9e0b58-ed6e-4db6-b47f-bfc2591780be_files'", "user_email": "tests@fake.org", "command_version": "R version 4.3.2 (2023-10-31) -- \"Eye Holes\", limma version 3.58.1, edgeR version 4.0.2, statmod version 1.5.0, scales version 1.3.0, rjson version 0.2.21, getopt version 1.20.4, gplots version 3.1.3.1, Glimma version 2.12.0", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"lfc\": \"0.0\", \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true, \"topgenes\": \"6\", \"treat\": false}", "out": "{\"filtCounts\": false, \"libinfo\": false, \"normCounts\": false, \"plots\": \"i\", \"rdaOption\": false, \"rscript\": false}", "f": "{\"filt\": {\"__current_case__\": 1, \"filt_select\": \"no\"}}", "cont": "{\"__current_case__\": 0, \"cfile\": \"yes\", \"cinfo\": {\"values\": [{\"id\": 138, \"src\": \"hda\"}]}}", "anno": "{\"__current_case__\": 1, \"annoOpt\": \"no\"}", "input": "{\"__current_case__\": 1, \"counts\": {\"values\": [{\"id\": 137, \"src\": \"hda\"}]}, \"fact\": {\"__current_case__\": 1, \"ffile\": \"no\", \"rep_factor\": [{\"__index__\": 0, \"factorName\": 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{"outTables": {"src": "hdca", "id": "ee2b038af4efbd73"}}, "tool_stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_stdout": "", "job_stderr": "", "stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "24 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "24.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:01:55", "plugin": "core", "name": "end_epoch", "raw_value": "1727290915.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:01:31", "plugin": "core", "name": "start_epoch", "raw_value": "1727290891.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "limma_voom/3.58.1+galaxy0-2", "has_data": true, "data": {"tool_id": 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'/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/c/8/e/dataset_c8e6c0b5-dfd1-4990-87e4-d805e3e52778.dat' -o '/galaxy/server/database/objects/c/8/e/dataset_c8e6c0b5-dfd1-4990-87e4-d805e3e52778_files' -m '/galaxy/server/database/objects/0/a/6/dataset_0a60ee11-f5d7-4555-97b7-bab921a017cc.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -D 'Mut-WT' -P i -r -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/c/8/e/dataset_c8e6c0b5-dfd1-4990-87e4-d805e3e52778_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/c/8/e/dataset_c8e6c0b5-dfd1-4990-87e4-d805e3e52778_files' && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/119b069fc845/limma_voom/limma_voom.R' '/galaxy/server/database/objects/f/8/1/dataset_f8137b97-66ad-47b9-b494-2384f6bf1540.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"lfc\": \"0.0\", \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true, \"topgenes\": \"6\", \"treat\": false}", "out": "{\"filtCounts\": false, \"libinfo\": false, \"normCounts\": false, \"plots\": \"i\", \"rdaOption\": true, \"rscript\": true}", "f": "{\"filt\": {\"__current_case__\": 1, \"filt_select\": \"no\"}}", "cont": "{\"__current_case__\": 1, \"cfile\": \"no\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": \"Mut-WT\"}]}", "anno": "{\"__current_case__\": 1, \"annoOpt\": \"no\"}", "input": "{\"__current_case__\": 1, \"counts\": {\"values\": [{\"id\": 50, \"src\": \"hda\"}]}, \"fact\": {\"__current_case__\": 1, \"ffile\": \"no\", \"rep_factor\": [{\"__index__\": 0, \"factorName\": \"Genotype\", \"groupNames\": \"Mut,Mut,Mut,WT,WT,WT\"}]}, \"format\": \"matrix\"}", 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Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n[1] \"Saving RData\"\n", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_stdout": "", "job_stderr": "", "stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n[1] \"Saving RData\"\n", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", 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Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:45:05", "plugin": "core", "name": "start_epoch", "raw_value": "1727289905.0000000"}, {"title": "Job End Time", "value": "2024-09-25 18:45:28", "plugin": "core", "name": "end_epoch", "raw_value": "1727289928.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "23 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "23.0000000"}]}, "status": "success"}}, 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Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:46:07", "plugin": "core", "name": "start_epoch", "raw_value": "1727289967.0000000"}, {"title": "Job End Time", "value": "2024-09-25 18:46:31", "plugin": "core", "name": "end_epoch", "raw_value": "1727289991.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "24 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": 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\"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_stdout": "", "job_stderr": "", "stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "24 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": 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request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Outputting filtered counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_stdout": "", "job_stderr": "", "stdout": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Outputting filtered counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", 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\"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "24 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "24.0000000"}, {"title": "Job End Time", "value": "2024-09-25 18:57:59", "plugin": "core", "name": "end_epoch", "raw_value": "1727290679.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:57:35", "plugin": "core", "name": "start_epoch", "raw_value": "1727290655.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", 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\"en_US.UTF-8\" cannot be honored\n[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "23 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "23.0000000"}, {"title": "Job End Time", "value": "2024-09-25 18:49:32", "plugin": "core", "name": "end_epoch", "raw_value": "1727290172.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:49:09", "plugin": "core", "name": "start_epoch", "raw_value": "1727290149.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": 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\"www.lab.not.exist\"}", "metadata": "[{\"__index__\": 0, \"label_desc\": \"Patient gender\", \"row_names\": \"gender\"}, {\"__index__\": 1, \"label_desc\": \"Case/control status\", \"row_names\": \"type\"}, {\"__index__\": 2, \"label_desc\": \"Tumor Progress on XYZ scale\", \"row_names\": \"score\"}]", "annotation": "\"hgu95av2\""}, "inputs": {"exprs_file": {"id": "8970d1187d6ee4e3", "src": "hda", "uuid": "8c741297-978b-46e6-912a-31e53d279bf9"}, "pdata_file": {"id": "e69c2b3720943dd4", "src": "hda", "uuid": "1aab4e58-8554-481b-acd5-5846b64c1eff"}}, "outputs": {"out_rds": {"id": "826345b6d8739074", "src": "hda", "uuid": "9489797a-0139-4dcb-968d-7dcf682b1bb2"}, "out_tab": {"id": "16f084dc7582ea60", "src": "hda", "uuid": "b0d428d0-0bf6-43d9-b7d3-0944d265c156"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, 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"command_line": "porechop -i '/galaxy/server/database/objects/1/0/b/dataset_10be18c5-10fb-4a74-86d5-624a48420b42.dat' --format 'fasta' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fasta'", "user_email": "tests@fake.org", "command_version": "0.2.4", "params": {"format": "\"fasta\"", "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input_file": {"id": "0c3c3ef59067322a", "src": "hda", "uuid": "10be18c5-10fb-4a74-86d5-624a48420b42"}}, "outputs": {"outfile": {"id": "2a5d6975d93331b5", "src": "hda", "uuid": "011ed9c6-25b1-40be-8199-59293b58e5f3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/1/0/b/dataset_10be18c5-10fb-4a74-86d5-624a48420b42.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/22/working/out.fasta\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/1/0/b/dataset_10be18c5-10fb-4a74-86d5-624a48420b42.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/22/working/out.fasta\n\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:38:37", "plugin": "core", "name": "start_epoch", "raw_value": "1727289517.0000000"}, {"title": "Job End Time", "value": "2024-09-25 18:38:38", "plugin": "core", "name": "end_epoch", "raw_value": "1727289518.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "porechop/0.2.4+galaxy0-1", "has_data": true, "data": {"tool_id": "porechop", "tool_version": "0.2.4+galaxy0", "test_index": 1, "time_seconds": 38.14934825897217, "inputs": {"input_file": {"src": "hda", "id": "0076c240c1215f91"}, "format": "fastq"}, "job": {"model_class": "Job", "id": "8b62c289ec63f46c", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T18:39:14.829622", "update_time": "2024-09-25T18:39:30.390363", "galaxy_version": "24.1", "external_id": "gxy-pbn2l", "handler": null, "job_runner_name": null, "command_line": "porechop -i '/galaxy/server/database/objects/9/b/0/dataset_9b03c0f7-ab8b-408d-bb14-d325e2734449.dat' --format 'fastq' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fastq'", "user_email": "tests@fake.org", "command_version": "0.2.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", "format": "\"fastq\""}, "inputs": {"input_file": {"id": "0076c240c1215f91", "src": "hda", "uuid": "9b03c0f7-ab8b-408d-bb14-d325e2734449"}}, "outputs": {"outfile": {"id": "24f4a942c09aed0a", "src": "hda", "uuid": "dd602d1b-2f6b-40e8-9ead-7f8b9286f874"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/9/b/0/dataset_9b03c0f7-ab8b-408d-bb14-d325e2734449.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/24/working/out.fastq\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/9/b/0/dataset_9b03c0f7-ab8b-408d-bb14-d325e2734449.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/24/working/out.fastq\n\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:39:16", "plugin": "core", "name": "start_epoch", "raw_value": "1727289556.0000000"}, {"title": "Job End Time", "value": "2024-09-25 18:39:17", "plugin": "core", "name": "end_epoch", "raw_value": "1727289557.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "porechop/0.2.4+galaxy0-2", "has_data": true, "data": {"tool_id": "porechop", "tool_version": "0.2.4+galaxy0", "test_index": 2, "time_seconds": 26.897997617721558, "inputs": {"input_file": {"src": "hda", "id": "e5551c944ebef800"}, "format": "fastq"}, "job": {"model_class": "Job", "id": "271fdef17e8ec9e0", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0", "state": "error", "exit_code": null, "create_time": "2024-09-25T18:39:53.021927", "update_time": "2024-09-25T18:39:57.805896", "galaxy_version": "24.1", "external_id": "gxy-z76bg", "handler": null, "job_runner_name": null, "command_line": "porechop -i '/galaxy/server/database/objects/b/e/d/dataset_bed07ad6-cd8a-4669-b60f-4850db752d72.dat' --format 'fastq' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fastq'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", "format": "\"fastq\""}, "inputs": {"input_file": {"id": "e5551c944ebef800", "src": "hda", "uuid": "bed07ad6-cd8a-4669-b60f-4850db752d72"}}, "outputs": {"outfile": {"id": "6e8c2795f7763819", "src": "hda", "uuid": "bf78ed51-bab5-41ec-bdd6-ad981690898c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/b/e/d/dataset_bed07ad6-cd8a-4669-b60f-4850db752d72.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/26/working/out.fastq\n\n", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/b/e/d/dataset_bed07ad6-cd8a-4669-b60f-4850db752d72.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/26/working/out.fastq\n\n", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "porechop/0.2.4+galaxy0-3", "has_data": true, "data": {"tool_id": "porechop", "tool_version": "0.2.4+galaxy0", "test_index": 3, "time_seconds": 36.54365015029907, "inputs": {"input_file": {"src": "hda", "id": "4402183547455a00"}, "format": "fasta.gz"}, "job": {"model_class": "Job", "id": "4c8069bbcc63e6f4", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T18:40:19.368418", "update_time": "2024-09-25T18:40:34.145483", "galaxy_version": "24.1", "external_id": "gxy-qcdms", "handler": null, "job_runner_name": null, "command_line": "porechop -i '/galaxy/server/database/objects/8/2/2/dataset_82243fca-e9b1-41c3-881d-49f6f7272aa6.dat' --format 'fasta.gz' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fasta.gz'", "user_email": "tests@fake.org", "command_version": "0.2.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", "format": "\"fasta.gz\""}, "inputs": {"input_file": {"id": "4402183547455a00", "src": "hda", "uuid": "82243fca-e9b1-41c3-881d-49f6f7272aa6"}}, "outputs": {"outfile": {"id": "3a933a363efcc777", "src": "hda", "uuid": "43ec8daf-91a9-4383-b0e6-030ad99a85b1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/8/2/2/dataset_82243fca-e9b1-41c3-881d-49f6f7272aa6.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\npigz not found - using gzip to compress\n\nSaved result to /galaxy/server/database/jobs_directory/000/28/working/out.fasta.gz\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/8/2/2/dataset_82243fca-e9b1-41c3-881d-49f6f7272aa6.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\npigz not found - using gzip to compress\n\nSaved result to /galaxy/server/database/jobs_directory/000/28/working/out.fasta.gz\n\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:40:20", "plugin": "core", "name": "start_epoch", "raw_value": "1727289620.0000000"}, {"title": "Job End Time", "value": "2024-09-25 18:40:21", "plugin": "core", "name": "end_epoch", "raw_value": "1727289621.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "porechop/0.2.4+galaxy0-4", "has_data": true, "data": {"tool_id": "porechop", "tool_version": "0.2.4+galaxy0", "test_index": 4, "time_seconds": 38.57286286354065, "inputs": {"input_file": {"src": "hda", "id": "c0acbba0e0108e01"}, "format": "fastq.gz"}, "job": {"model_class": "Job", "id": "2bb154aea9ac98f7", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T18:40:56.710519", "update_time": "2024-09-25T18:41:12.778710", "galaxy_version": "24.1", "external_id": "gxy-7x9jq", "handler": null, "job_runner_name": null, "command_line": "porechop -i '/galaxy/server/database/objects/f/7/f/dataset_f7f9e208-0efa-4377-84ad-5ac92c2d4083.dat' --format 'fastq.gz' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fastq.gz'", "user_email": "tests@fake.org", "command_version": "0.2.4", "params": {"format": "\"fastq.gz\"", "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input_file": {"id": "c0acbba0e0108e01", "src": "hda", "uuid": "f7f9e208-0efa-4377-84ad-5ac92c2d4083"}}, "outputs": {"outfile": {"id": "65f054e375d40251", "src": "hda", "uuid": "b3568aef-b43e-4ec7-9fc3-3e800a7b824e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/f/7/f/dataset_f7f9e208-0efa-4377-84ad-5ac92c2d4083.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\npigz not found - using gzip to compress\n\nSaved result to /galaxy/server/database/jobs_directory/000/30/working/out.fastq.gz\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/f/7/f/dataset_f7f9e208-0efa-4377-84ad-5ac92c2d4083.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR adapters 2 66.7 63.6\n PCR adapters 3 68.0 72.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n cDNA SSP 57.1 61.4\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\npigz not found - using gzip to compress\n\nSaved result to /galaxy/server/database/jobs_directory/000/30/working/out.fastq.gz\n\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 18:40:59", "plugin": "core", "name": "start_epoch", "raw_value": "1727289659.0000000"}, {"title": "Job End Time", "value": "2024-09-25 18:41:00", "plugin": "core", "name": "end_epoch", "raw_value": "1727289660.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "porechop/0.2.4+galaxy0-5", "has_data": true, "data": {"tool_id": "porechop", "tool_version": "0.2.4+galaxy0", "test_index": 5, "time_seconds": 37.4209771156311, "inputs": {"input_file": {"src": "hda", "id": "6adb81f00ec0efae"}, "format": "fasta", "barcode_binning_settings|barcode_threshold": "70", "barcode_binning_settings|barcode_diff": "4", "barcode_binning_settings|require_two_barcodes": true, "barcode_binning_settings|discard_unassigned": true, "end_adapter_settings|end_size": "100", "end_adapter_settings|min_trim_size": "2", "end_adapter_settings|extra_end_trim": "1", "end_adapter_settings|end_threshold": "80", "middle_adapter_settings|discard_middle": true, "middle_adapter_settings|middle_threshold": "90", "middle_adapter_settings|min_split_read_size": "1500"}, "job": {"model_class": "Job", "id": "0c3c3ef59067322a", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T18:41:35.384440", "update_time": "2024-09-25T18:41:50.021526", "galaxy_version": "24.1", "external_id": "gxy-5bk6s", "handler": null, "job_runner_name": null, "command_line": "porechop -i '/galaxy/server/database/objects/2/e/6/dataset_2e6a7958-6a89-4739-a982-0f50dd2e54a9.dat' --format 'fasta' --barcode_threshold '70.0' --barcode_diff '4.0' --require_two_barcodes --discard_unassigned --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '100' --min_trim_size '2' --extra_end_trim '1' --end_threshold '80.0' --discard_middle --middle_threshold '90.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1500' -o 'out.fasta'", "user_email": "tests@fake.org", "command_version": "0.2.4", "params": {"format": "\"fasta\"", "barcode_binning_settings": "{\"barcode_diff\": \"4.0\", \"barcode_threshold\": \"70.0\", \"discard_unassigned\": true, \"require_two_barcodes\": true}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "end_adapter_settings": "{\"end_size\": \"100\", \"end_threshold\": \"80.0\", \"extra_end_trim\": \"1\", \"min_trim_size\": \"2\"}", "middle_adapter_settings": "{\"discard_middle\": true, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"90.0\", \"min_split_read_size\": \"1500\", \"no_split\": false}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"input_file": {"id": "6adb81f00ec0efae", "src": "hda", "uuid": "2e6a7958-6a89-4739-a982-0f50dd2e54a9"}}, "outputs": {"outfile": {"id": "3b640eeae998f5cf", "src": "hda", "uuid": "0a05b53c-8d40-4539-9baa-5498f2e763c7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/2/e/6/dataset_2e6a7958-6a89-4739-a982-0f50dd2e54a9.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 58.8 63.6\n SQK-MAP006 short 58.6 57.7\n PCR adapters 1 66.7 73.9\n PCR adapters 2 65.4 63.6\n PCR adapters 3 68.0 70.4\n 1D^2 part 1 66.7 58.6\n 1D^2 part 2 79.4 68.8\n cDNA SSP 58.7 61.4\n Barcode 1 (reverse) 58.3 66.7\n Barcode 2 (reverse) 66.7 50.0\n Barcode 3 (reverse) 69.2 69.2\n Barcode 4 (reverse) 66.7 61.5\n Barcode 5 (reverse) 62.5 69.2\n Barcode 6 (reverse) 65.4 62.5\n Barcode 7 (reverse) 62.5 65.5\n Barcode 8 (reverse) 59.3 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 57.7 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 55.2\n Barcode 1 (forward) 65.4 62.1\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 65.4 68.0\n Barcode 4 (forward) 63.3 64.3\n Barcode 5 (forward) 57.1 56.0\n Barcode 6 (forward) 45.7 63.0\n Barcode 7 (forward) 73.1 62.1\n Barcode 8 (forward) 62.1 60.6\n Barcode 9 (forward) 64.3 66.7\n Barcode 10 (forward) 61.8 68.0\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 60.6 66.7\n Barcode 13 (forward) 64.5 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 65.5 64.0\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 64.0\n Barcode 19 (forward) 64.5 63.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 57.9 65.5\n Barcode 24 (forward) 66.7 61.3\n Barcode 25 (forward) 59.4 68.0\n Barcode 26 (forward) 64.3 72.0\n Barcode 27 (forward) 61.3 59.4\n Barcode 28 (forward) 65.4 62.5\n Barcode 29 (forward) 57.7 62.5\n Barcode 30 (forward) 68.0 64.0\n Barcode 31 (forward) 62.1 61.5\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 46.2 70.4\n Barcode 34 (forward) 64.0 18.5\n Barcode 35 (forward) 64.3 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 61.5 62.5\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 62.5\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 66.7 60.7\n Barcode 47 (forward) 64.3 61.5\n Barcode 48 (forward) 71.4 65.4\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 57.1\n Barcode 51 (forward) 69.2 59.3\n Barcode 52 (forward) 62.5 64.0\n Barcode 53 (forward) 65.4 69.0\n Barcode 54 (forward) 69.2 62.1\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 62.5 64.0\n Barcode 57 (forward) 66.7 55.6\n Barcode 58 (forward) 67.7 66.7\n Barcode 59 (forward) 56.7 59.4\n Barcode 60 (forward) 66.7 63.0\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 62.5\n Barcode 64 (forward) 60.7 67.9\n Barcode 65 (forward) 61.5 62.5\n Barcode 66 (forward) 61.5 61.3\n Barcode 67 (forward) 66.7 60.0\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 65.5 66.7\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 60.7 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 63.6\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 60.6 64.0\n Barcode 77 (forward) 65.4 62.1\n Barcode 78 (forward) 66.7 63.3\n Barcode 79 (forward) 70.8 66.7\n Barcode 80 (forward) 62.5 66.7\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.0 66.7\n Barcode 83 (forward) 64.0 68.0\n Barcode 84 (forward) 64.5 67.9\n Barcode 85 (forward) 61.5 58.3\n Barcode 86 (forward) 64.3 66.7\n Barcode 87 (forward) 66.7 65.5\n Barcode 88 (forward) 63.3 61.5\n Barcode 89 (forward) 69.0 66.7\n Barcode 90 (forward) 64.3 61.3\n Barcode 91 (forward) 53.3 64.0\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 63.3 71.4\n Barcode 94 (forward) 61.5 64.5\n Barcode 95 (forward) 62.1 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (70 bp removed)\n3 / 9 reads had adapters trimmed from their end (46 bp removed)\n\n\n\u001b[1m\u001b[4mDiscarding reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were discarded based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/32/working/out.fasta\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/2/e/6/dataset_2e6a7958-6a89-4739-a982-0f50dd2e54a9.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n RBK004_upstream 72.7 0.0\n SQK-MAP006 58.8 63.6\n SQK-MAP006 short 58.6 57.7\n PCR adapters 1 66.7 73.9\n PCR adapters 2 65.4 63.6\n PCR adapters 3 68.0 70.4\n 1D^2 part 1 66.7 58.6\n 1D^2 part 2 79.4 68.8\n cDNA SSP 58.7 61.4\n Barcode 1 (reverse) 58.3 66.7\n Barcode 2 (reverse) 66.7 50.0\n Barcode 3 (reverse) 69.2 69.2\n Barcode 4 (reverse) 66.7 61.5\n Barcode 5 (reverse) 62.5 69.2\n Barcode 6 (reverse) 65.4 62.5\n Barcode 7 (reverse) 62.5 65.5\n Barcode 8 (reverse) 59.3 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 57.7 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 55.2\n Barcode 1 (forward) 65.4 62.1\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 65.4 68.0\n Barcode 4 (forward) 63.3 64.3\n Barcode 5 (forward) 57.1 56.0\n Barcode 6 (forward) 45.7 63.0\n Barcode 7 (forward) 73.1 62.1\n Barcode 8 (forward) 62.1 60.6\n Barcode 9 (forward) 64.3 66.7\n Barcode 10 (forward) 61.8 68.0\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 60.6 66.7\n Barcode 13 (forward) 64.5 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 65.5 64.0\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 64.0\n Barcode 19 (forward) 64.5 63.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 57.9 65.5\n Barcode 24 (forward) 66.7 61.3\n Barcode 25 (forward) 59.4 68.0\n Barcode 26 (forward) 64.3 72.0\n Barcode 27 (forward) 61.3 59.4\n Barcode 28 (forward) 65.4 62.5\n Barcode 29 (forward) 57.7 62.5\n Barcode 30 (forward) 68.0 64.0\n Barcode 31 (forward) 62.1 61.5\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 46.2 70.4\n Barcode 34 (forward) 64.0 18.5\n Barcode 35 (forward) 64.3 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 61.5 62.5\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 62.5\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 66.7 60.7\n Barcode 47 (forward) 64.3 61.5\n Barcode 48 (forward) 71.4 65.4\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 57.1\n Barcode 51 (forward) 69.2 59.3\n Barcode 52 (forward) 62.5 64.0\n Barcode 53 (forward) 65.4 69.0\n Barcode 54 (forward) 69.2 62.1\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 62.5 64.0\n Barcode 57 (forward) 66.7 55.6\n Barcode 58 (forward) 67.7 66.7\n Barcode 59 (forward) 56.7 59.4\n Barcode 60 (forward) 66.7 63.0\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 62.5\n Barcode 64 (forward) 60.7 67.9\n Barcode 65 (forward) 61.5 62.5\n Barcode 66 (forward) 61.5 61.3\n Barcode 67 (forward) 66.7 60.0\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 65.5 66.7\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 60.7 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 63.6\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 60.6 64.0\n Barcode 77 (forward) 65.4 62.1\n Barcode 78 (forward) 66.7 63.3\n Barcode 79 (forward) 70.8 66.7\n Barcode 80 (forward) 62.5 66.7\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.0 66.7\n Barcode 83 (forward) 64.0 68.0\n Barcode 84 (forward) 64.5 67.9\n Barcode 85 (forward) 61.5 58.3\n Barcode 86 (forward) 64.3 66.7\n Barcode 87 (forward) 66.7 65.5\n Barcode 88 (forward) 63.3 61.5\n Barcode 89 (forward) 69.0 66.7\n Barcode 90 (forward) 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"1727291140.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.9.6+galaxy4-0", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.9.6+galaxy4", "test_index": 0, "time_seconds": 81.89430403709412, "inputs": {"adata": {"src": "hda", "id": "0a10c9179e291645"}, "method|filter|min_counts": "3", "method|filter|filter": "min_counts", "method|method": "pp.filter_cells", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "db3b85bf0719e28e", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:16:35.772692", "update_time": "2024-09-25T19:17:34.040805", "galaxy_version": "24.1", "external_id": "gxy-m5cgv", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/4/1/0/dataset_410a64e4-3754-490b-af75-6f62ea540c72.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/135/configs/tmpmmfvz2ab' > '/galaxy/server/database/objects/a/3/3/dataset_a3353923-ff2a-40ec-9467-574717a5056a.dat' && python '/galaxy/server/database/jobs_directory/000/135/configs/tmpmmfvz2ab' >> '/galaxy/server/database/objects/a/3/3/dataset_a3353923-ff2a-40ec-9467-574717a5056a.dat' && ls . >> '/galaxy/server/database/objects/a/3/3/dataset_a3353923-ff2a-40ec-9467-574717a5056a.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 0, \"filter\": {\"__current_case__\": 0, \"filter\": \"min_counts\", \"min_counts\": \"3\"}, \"method\": \"pp.filter_cells\"}"}, "inputs": {"adata": {"id": "0a10c9179e291645", "src": "hda", "uuid": "410a64e4-3754-490b-af75-6f62ea540c72"}}, "outputs": {"anndata_out": {"id": "bf668bedee502123", "src": "hda", "uuid": "8aacda55-ada9-4be4-80cc-08ac488cb852"}, "hidden_output": {"id": "a36ba78bbf6f884f", "src": "hda", "uuid": "a3353923-ff2a-40ec-9467-574717a5056a"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 336 \u00d7 11\n[obs]\n- cell_type\n- n_counts\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 336 \u00d7 11\n[obs]\n- cell_type\n- n_counts\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:17:11", "plugin": "core", "name": "end_epoch", "raw_value": "1727291831.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:17:06", "plugin": "core", "name": "start_epoch", "raw_value": "1727291826.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.9.6+galaxy4-1", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.9.6+galaxy4", "test_index": 1, "time_seconds": 43.28046655654907, "inputs": {"adata": {"src": "hda", "id": "485eb734f0ba54cf"}, "method|filter|max_genes": "100", "method|filter|filter": "max_genes", "method|method": "pp.filter_cells", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "0a07a0475d30bf5e", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:17:57.253670", "update_time": "2024-09-25T19:18:17.425403", "galaxy_version": "24.1", "external_id": "gxy-5dqlb", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/2/e/5/dataset_2e525cfc-8e81-46f7-a582-eb887da94745.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/137/configs/tmp2fyx6ddj' > '/galaxy/server/database/objects/7/8/7/dataset_78761104-623b-40a2-9dcb-1936f671eaf1.dat' && python '/galaxy/server/database/jobs_directory/000/137/configs/tmp2fyx6ddj' >> '/galaxy/server/database/objects/7/8/7/dataset_78761104-623b-40a2-9dcb-1936f671eaf1.dat' && ls . >> '/galaxy/server/database/objects/7/8/7/dataset_78761104-623b-40a2-9dcb-1936f671eaf1.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 0, \"filter\": {\"__current_case__\": 3, \"filter\": \"max_genes\", \"max_genes\": \"100\"}, \"method\": \"pp.filter_cells\"}"}, "inputs": {"adata": {"id": "485eb734f0ba54cf", "src": "hda", "uuid": "2e525cfc-8e81-46f7-a582-eb887da94745"}}, "outputs": {"anndata_out": {"id": "77555eb8bbf6ac18", "src": "hda", "uuid": "3a172751-0c62-492d-bdeb-e48742e3b28d"}, "hidden_output": {"id": "67436112237c35c5", "src": "hda", "uuid": "78761104-623b-40a2-9dcb-1936f671eaf1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n- n_genes\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n- n_genes\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:18:04", "plugin": "core", "name": "end_epoch", "raw_value": "1727291884.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:17:59", "plugin": "core", "name": "start_epoch", "raw_value": "1727291879.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.9.6+galaxy4-2", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.9.6+galaxy4", "test_index": 2, "time_seconds": 42.55212116241455, "inputs": {"adata": {"src": "hda", "id": "de07d76736f6504c"}, "method|filter|min_counts": "3", "method|filter|filter": "min_counts", "method|method": "pp.filter_genes", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "9e17675fffc30dc8", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:18:39.918036", "update_time": "2024-09-25T19:19:00.056352", "galaxy_version": "24.1", "external_id": "gxy-wz24z", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/2/f/1/dataset_2f1810ca-4d92-4196-8200-a07dbb32f1d2.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/139/configs/tmp65ifvtn3' > '/galaxy/server/database/objects/8/c/8/dataset_8c8cf981-4173-4e13-8e4f-6790431fb6f6.dat' && python '/galaxy/server/database/jobs_directory/000/139/configs/tmp65ifvtn3' >> '/galaxy/server/database/objects/8/c/8/dataset_8c8cf981-4173-4e13-8e4f-6790431fb6f6.dat' && ls . >> '/galaxy/server/database/objects/8/c/8/dataset_8c8cf981-4173-4e13-8e4f-6790431fb6f6.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 1, \"filter\": {\"__current_case__\": 0, \"filter\": \"min_counts\", \"min_counts\": \"3\"}, \"method\": \"pp.filter_genes\"}"}, "inputs": {"adata": {"id": "de07d76736f6504c", "src": "hda", "uuid": "2f1810ca-4d92-4196-8200-a07dbb32f1d2"}}, "outputs": {"anndata_out": {"id": "a24221edaa7f5baa", "src": "hda", "uuid": "0718ada3-95f8-4c6f-bcad-715f86a62eb7"}, "hidden_output": {"id": "c72c7cd141ddbde7", "src": "hda", "uuid": "8c8cf981-4173-4e13-8e4f-6790431fb6f6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[var]\n- n_counts\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[var]\n- n_counts\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:18:47", "plugin": "core", "name": "end_epoch", "raw_value": "1727291927.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:18:41", "plugin": "core", "name": "start_epoch", "raw_value": "1727291921.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.9.6+galaxy4-3", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.9.6+galaxy4", "test_index": 3, "time_seconds": 43.21078109741211, "inputs": {"adata": {"src": "hda", "id": "828d96d6a49dcb2f"}, "method|flavor|min_mean": "0.0125", "method|flavor|max_mean": "3", "method|flavor|min_disp": "0.5", "method|flavor|flavor": "seurat", "method|n_bins": "20", "method|subset": false, "method|method": "pp.highly_variable_genes", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "41495940fbf8a097", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:19:23.445924", "update_time": "2024-09-25T19:19:43.346111", "galaxy_version": "24.1", "external_id": "gxy-7tpnc", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/5/3/4/dataset_53404ce2-faf0-40a4-af50-4c0ac0440ac3.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/141/configs/tmpkbhpes64' > '/galaxy/server/database/objects/c/d/b/dataset_cdbc4bfd-6ccb-431c-9d02-e234e8821341.dat' && python '/galaxy/server/database/jobs_directory/000/141/configs/tmpkbhpes64' >> '/galaxy/server/database/objects/c/d/b/dataset_cdbc4bfd-6ccb-431c-9d02-e234e8821341.dat' && ls . >> '/galaxy/server/database/objects/c/d/b/dataset_cdbc4bfd-6ccb-431c-9d02-e234e8821341.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 3, \"flavor\": {\"__current_case__\": 0, \"flavor\": \"seurat\", \"max_disp\": \"\", \"max_mean\": \"3.0\", \"min_disp\": \"0.5\", \"min_mean\": \"0.0125\"}, \"method\": \"pp.highly_variable_genes\", \"n_bins\": \"20\", \"subset\": false}"}, "inputs": {"adata": {"id": "828d96d6a49dcb2f", "src": "hda", "uuid": "53404ce2-faf0-40a4-af50-4c0ac0440ac3"}}, "outputs": {"anndata_out": {"id": "7a621d657db1f4b9", "src": "hda", "uuid": "903a4dac-3918-4684-91d5-8a75c7148e0e"}, "hidden_output": {"id": "de17a4ed56b4a673", "src": "hda", "uuid": "cdbc4bfd-6ccb-431c-9d02-e234e8821341"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- blobs\n[var]\n- highly_variable\n- means\n- dispersions\n- dispersions_norm\n[uns]\n- hvg\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- blobs\n[var]\n- highly_variable\n- means\n- dispersions\n- dispersions_norm\n[uns]\n- hvg\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:19:30", "plugin": "core", "name": "end_epoch", "raw_value": "1727291970.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:19:24", "plugin": "core", "name": "start_epoch", "raw_value": "1727291964.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.9.6+galaxy4-4", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.9.6+galaxy4", "test_index": 4, "time_seconds": 42.76695728302002, "inputs": {"adata": {"src": "hda", "id": "b98785ad821d01f5"}, "method|flavor|n_top_genes": "2", "method|flavor|flavor": "cell_ranger", "method|n_bins": "20", "method|subset": true, "method|method": "pp.highly_variable_genes", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "1657fdfccce8835b", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:20:06.340994", "update_time": "2024-09-25T19:20:26.204790", "galaxy_version": "24.1", "external_id": "gxy-cxlwf", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/2/c/4/dataset_2c4f2db4-407f-4b06-936b-f3620c8775a6.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/143/configs/tmp7ped6d_z' > '/galaxy/server/database/objects/8/2/1/dataset_821f1ddc-3b95-4d8c-b919-a9ef4b0248e7.dat' && python '/galaxy/server/database/jobs_directory/000/143/configs/tmp7ped6d_z' >> '/galaxy/server/database/objects/8/2/1/dataset_821f1ddc-3b95-4d8c-b919-a9ef4b0248e7.dat' && ls . >> '/galaxy/server/database/objects/8/2/1/dataset_821f1ddc-3b95-4d8c-b919-a9ef4b0248e7.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 3, \"flavor\": {\"__current_case__\": 1, \"flavor\": \"cell_ranger\", \"n_top_genes\": \"2\"}, \"method\": \"pp.highly_variable_genes\", \"n_bins\": \"20\", \"subset\": true}"}, "inputs": {"adata": {"id": "b98785ad821d01f5", "src": "hda", "uuid": "2c4f2db4-407f-4b06-936b-f3620c8775a6"}}, "outputs": {"anndata_out": {"id": "93219fbcd3cc5dbf", "src": "hda", "uuid": "eec84293-1bb1-4524-b2c7-b9b2e0046be0"}, "hidden_output": {"id": "3c0802fcbcde8c62", "src": "hda", "uuid": "821f1ddc-3b95-4d8c-b919-a9ef4b0248e7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[var]\n- highly_variable\n- means\n- dispersions\n- dispersions_norm\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n- hvg\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[var]\n- highly_variable\n- means\n- dispersions\n- dispersions_norm\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n- hvg\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:20:13", "plugin": "core", "name": "end_epoch", "raw_value": "1727292013.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:20:07", "plugin": "core", "name": "start_epoch", "raw_value": "1727292007.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.9.6+galaxy4-5", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.9.6+galaxy4", "test_index": 5, "time_seconds": 42.00015926361084, "inputs": {"adata": {"src": "hda", "id": "0789fd95fddff4c5"}, "method|type|fraction": "0.5", "method|type|type": "fraction", "method|random_state": "0", "method|method": "pp.subsample", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "d072ab4e1c8a31e6", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:20:49.267741", "update_time": "2024-09-25T19:21:08.085537", "galaxy_version": "24.1", "external_id": "gxy-kmfzj", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/3/7/7/dataset_3771d574-c4d3-4dbc-8c84-923acfd87009.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/145/configs/tmp19husl8e' > '/galaxy/server/database/objects/f/2/0/dataset_f20f3489-d06a-4a63-a51e-e620e38103e8.dat' && python '/galaxy/server/database/jobs_directory/000/145/configs/tmp19husl8e' >> '/galaxy/server/database/objects/f/2/0/dataset_f20f3489-d06a-4a63-a51e-e620e38103e8.dat' && ls . >> '/galaxy/server/database/objects/f/2/0/dataset_f20f3489-d06a-4a63-a51e-e620e38103e8.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 4, \"method\": \"pp.subsample\", \"random_state\": \"0\", \"type\": {\"__current_case__\": 0, \"fraction\": \"0.5\", \"type\": \"fraction\"}}"}, "inputs": {"adata": {"id": "0789fd95fddff4c5", "src": "hda", "uuid": "3771d574-c4d3-4dbc-8c84-923acfd87009"}}, "outputs": {"anndata_out": {"id": "278be867b481b74b", "src": "hda", "uuid": "69511c88-8a3e-4617-8855-e1cb88073508"}, "hidden_output": {"id": "05b59752086d9f4f", "src": "hda", "uuid": "f20f3489-d06a-4a63-a51e-e620e38103e8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 320 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 320 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:20:56", "plugin": "core", "name": "end_epoch", "raw_value": "1727292056.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:20:50", "plugin": "core", "name": "start_epoch", "raw_value": "1727292050.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.9.6+galaxy4-6", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.9.6+galaxy4", "test_index": 6, "time_seconds": 43.32378053665161, "inputs": {"adata": {"src": "hda", "id": "f568b7247e833819"}, "method|type|n_obs": "10", "method|type|type": "n_obs", "method|random_state": "0", "method|method": "pp.subsample", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "9a8ca040a1e0d987", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:21:31.151744", "update_time": "2024-09-25T19:21:51.572432", "galaxy_version": "24.1", "external_id": "gxy-qrvsr", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/6/4/2/dataset_64202407-3ad6-46de-a1c9-1b569dad17e3.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/147/configs/tmp5eshq9nm' > '/galaxy/server/database/objects/0/e/8/dataset_0e831b9f-b779-4388-9ab2-ea5d0583dd5f.dat' && python '/galaxy/server/database/jobs_directory/000/147/configs/tmp5eshq9nm' >> '/galaxy/server/database/objects/0/e/8/dataset_0e831b9f-b779-4388-9ab2-ea5d0583dd5f.dat' && ls . >> '/galaxy/server/database/objects/0/e/8/dataset_0e831b9f-b779-4388-9ab2-ea5d0583dd5f.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 4, \"method\": \"pp.subsample\", \"random_state\": \"0\", \"type\": {\"__current_case__\": 1, \"n_obs\": \"10\", \"type\": \"n_obs\"}}"}, "inputs": {"adata": {"id": "f568b7247e833819", "src": "hda", "uuid": "64202407-3ad6-46de-a1c9-1b569dad17e3"}}, "outputs": {"anndata_out": {"id": "ac9d78e3dbe2bc63", "src": "hda", "uuid": "2b01801e-1358-4267-b367-75d34325c31f"}, "hidden_output": {"id": "d01c6c41e5ee0c68", "src": "hda", "uuid": "0e831b9f-b779-4388-9ab2-ea5d0583dd5f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 10 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 10 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:21:38", "plugin": "core", "name": "end_epoch", "raw_value": "1727292098.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:21:33", "plugin": "core", "name": "start_epoch", "raw_value": "1727292093.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.9.6+galaxy4-7", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.9.6+galaxy4", "test_index": 7, "time_seconds": 154.62589621543884, "inputs": {"adata": {"src": "hda", "id": "8ccf07fb22efbc68"}, "method|total_counts": "20000", "method|random_state": "0", "method|replace": false, "method|method": "pp.downsample_counts", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "aa7b0cdc4b19afb4", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:22:15.301405", "update_time": "2024-09-25T19:24:26.013863", "galaxy_version": "24.1", "external_id": "gxy-vgvv5", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/3/a/9/dataset_3a958b5b-5494-4ea6-aac2-0f756dc0782f.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/149/configs/tmpbimiecxt' > '/galaxy/server/database/objects/8/3/3/dataset_8334561e-1779-4043-b2c9-76904539de21.dat' && python '/galaxy/server/database/jobs_directory/000/149/configs/tmpbimiecxt' >> '/galaxy/server/database/objects/8/3/3/dataset_8334561e-1779-4043-b2c9-76904539de21.dat' && ls . >> '/galaxy/server/database/objects/8/3/3/dataset_8334561e-1779-4043-b2c9-76904539de21.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 5, \"counts_per_cell\": \"\", \"method\": \"pp.downsample_counts\", \"random_state\": \"0\", \"replace\": false, \"total_counts\": \"20000\"}"}, "inputs": {"adata": {"id": "8ccf07fb22efbc68", "src": "hda", "uuid": "3a958b5b-5494-4ea6-aac2-0f756dc0782f"}}, "outputs": {"anndata_out": {"id": "f9fdf8e84e663c13", "src": "hda", "uuid": "26a3dd2c-8404-4df3-8fc2-c54aee65651e"}, "hidden_output": {"id": "2670d468cc7ccdf8", "src": "hda", "uuid": "8334561e-1779-4043-b2c9-76904539de21"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 1000 \u00d7 1000\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 1000 \u00d7 1000\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "116.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:24:13", "plugin": "core", "name": "end_epoch", "raw_value": "1727292253.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:22:17", "plugin": "core", "name": "start_epoch", "raw_value": "1727292137.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.9.6+galaxy4-8", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.9.6+galaxy4", "test_index": 8, "time_seconds": 54.0707585811615, "inputs": {"adata": {"src": "hda", "id": "ac8409f535dbd10f"}, "method|markerfile": {"src": "hda", "id": "8badc81ffac91a55"}, "method|thresh_mean": "1.0", "method|thresh_frac": "0.2", "method|groupby": "bulk_labels", "method|method": "filter_marker", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "257ddd70f7492f14", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:24:53.944436", "update_time": "2024-09-25T19:25:19.782760", "galaxy_version": "24.1", "external_id": "gxy-2v896", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/f/b/d/dataset_fbd586a6-d779-495b-b4fa-d57d897d588c.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/152/configs/tmpv8zluxhq' > '/galaxy/server/database/objects/c/d/9/dataset_cd9a86e0-b570-4cdb-93c0-2f27854b1e54.dat' && python '/galaxy/server/database/jobs_directory/000/152/configs/tmpv8zluxhq' >> '/galaxy/server/database/objects/c/d/9/dataset_cd9a86e0-b570-4cdb-93c0-2f27854b1e54.dat' && ls . >> '/galaxy/server/database/objects/c/d/9/dataset_cd9a86e0-b570-4cdb-93c0-2f27854b1e54.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.9.6", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 6, \"groupby\": \"bulk_labels\", \"header\": \"included\", \"layer_selection\": {\"__current_case__\": 1, \"use_raw\": \"True\"}, \"markerfile\": {\"values\": [{\"id\": 219, \"src\": \"hda\"}]}, \"method\": \"filter_marker\", \"thresh_frac\": \"0.2\", \"thresh_mean\": \"1.0\"}"}, "inputs": {"adata": {"id": "ac8409f535dbd10f", "src": "hda", "uuid": "fbd586a6-d779-495b-b4fa-d57d897d588c"}, "method|markerfile": {"id": "8badc81ffac91a55", "src": "hda", "uuid": "d4efff7f-fad0-4114-a87d-b3848eeee274"}}, "outputs": {"anndata_out": {"id": "c496c1e91a9f4e35", "src": "hda", "uuid": "8379d3ad-8391-4d3a-a8f8-f241bea9f818"}, "hidden_output": {"id": "5d05298634418149", "src": "hda", "uuid": "cd9a86e0-b570-4cdb-93c0-2f27854b1e54"}, "marker_out": {"id": "407b8f0da0822d99", "src": "hda", "uuid": "031c914c-cc3f-4b4d-8305-14911e99a940"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 100 \u00d7 221\n[obs]\n- bulk_labels\n- n_genes\n- percent_mito\n- n_counts\n- louvain\n[uns]\n- cosg\n- rank_genes_groups\n[obsm]\n- X_pca\n- X_umap\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 100 \u00d7 221\n[obs]\n- bulk_labels\n- n_genes\n- percent_mito\n- n_counts\n- louvain\n[uns]\n- cosg\n- rank_genes_groups\n[obsm]\n- X_pca\n- X_umap\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "9 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "9.0000000"}, {"title": "Job End Time", "value": "2024-09-25 19:25:04", "plugin": "core", "name": "end_epoch", "raw_value": "1727292304.0000000"}, {"title": "Job Start Time", "value": "2024-09-25 19:24:55", "plugin": "core", "name": "start_epoch", "raw_value": "1727292295.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_normalise_data/1.9.3+galaxy0-0", "has_data": true, "data": {"tool_id": "scanpy_normalise_data", "tool_version": "1.9.3+galaxy0", "test_index": 0, "time_seconds": 0.1576070785522461, "execution_problem": "Input staging problem: Test input file (filter_genes.h5) cannot be found.", "status": "error"}}, {"id": "scanpy_normalise_data/1.9.3+galaxy0-0", "has_data": true, "data": {"tool_id": "scanpy_normalise_data", "tool_version": "1.9.3+galaxy0", "test_index": 0, "time_seconds": 0.159592866897583, "execution_problem": "Input staging problem: Test input file (filter_genes.h5) cannot be found.", "status": "error"}}, {"id": "vcfgeno2haplo/1.0.0_rc3+galaxy0-0", "has_data": true, "data": {"tool_id": "vcfgeno2haplo", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 0, "time_seconds": 46.768953800201416, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "9987a97cbf7b9b9f"}, "reference_source|input_vcf": {"src": "hda", "id": "8201bafdc569c44a"}, "reference_source|reference_source_selector": "history", "window_size": "5000", "output_option": true}, "job": {"model_class": "Job", "id": "0789fd95fddff4c5", "history_id": "beda644706419afa", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-25T19:44:21.782615", "update_time": "2024-09-25T19:44:43.581691", "galaxy_version": "24.1", "external_id": "gxy-bnxbq", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/e/b/1/dataset_eb10e4f7-db02-4453-a1c7-0bbb03d13eab.dat' 'localref.fa' && vcfgeno2haplo -o -w 5000 -r \"localref.fa\" \"/galaxy/server/database/objects/0/d/6/dataset_0d6a48ee-689e-400a-af6b-611c5192de5d.dat\" > \"/galaxy/server/database/objects/8/4/a/dataset_84a32d97-df3e-4eea-962e-f966be186c23.dat\"", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_option": "true", "window_size": "\"5000\"", "reference_source": "{\"__current_case__\": 1, \"input_vcf\": {\"values\": [{\"id\": 285, \"src\": \"hda\"}]}, \"ref_file\": {\"values\": [{\"id\": 284, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|ref_file": {"id": "9987a97cbf7b9b9f", "src": "hda", "uuid": "eb10e4f7-db02-4453-a1c7-0bbb03d13eab"}, "reference_source|input_vcf": {"id": "8201bafdc569c44a", "src": "hda", 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