From f974bcddc4f0e1cc71e7e200096b8ac20024f642 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 12 Nov 2024 19:34:13 +0000 Subject: [PATCH] Updating anvil-edge README for edge-24-11-12-18-17-1 --- reports/anvil-edge/README.md | 2 +- reports/anvil-edge/tool-tests/chunks.json | 10 +- .../edge-24-11-12-18-17-1/chunk.json | 7 + .../edge-24-11-12-18-17-1/chunk.txt | 25 + .../errors/029e02c70d71eef6.json | 99 ++ .../errors/131fdfbf0346cb1a.json | 45 + .../errors/22517353a62337da.json | 47 + .../errors/2e4c4b2409f06dfd.json | 45 + .../errors/300354dbb5b5c093.json | 45 + .../errors/361b9c563cfcdddf.json | 45 + .../errors/5e4710b2acc93880.json | 45 + .../errors/9a957b6f1413b47b.json | 45 + .../errors/e28001cc42f670cf.json | 45 + .../errors/eee892f340a734c7.json | 52 + .../errors/f5bebfbeb8d90cbe.json | 45 + .../errors/fd4a77e3c68c4733.json | 45 + .../edge-24-11-12-18-17-1/job-metrics.csv | 210 +++ .../tool-tests/edge-24-11-12-18-17-1/jobs.txt | 209 +++ .../edge-24-11-12-18-17-1/results.html | 291 +++++ .../edge-24-11-12-18-17-1/results.json | 1 + .../edge-24-11-12-18-17-1/results.xunit | 1128 +++++++++++++++++ .../edge-24-11-12-18-17-1/tools.yml | 127 ++ 22 files changed, 2607 insertions(+), 6 deletions(-) create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/chunk.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/chunk.txt create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/029e02c70d71eef6.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/131fdfbf0346cb1a.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/22517353a62337da.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/2e4c4b2409f06dfd.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/300354dbb5b5c093.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/361b9c563cfcdddf.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/5e4710b2acc93880.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/9a957b6f1413b47b.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/e28001cc42f670cf.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/eee892f340a734c7.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/f5bebfbeb8d90cbe.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/fd4a77e3c68c4733.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/job-metrics.csv create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/jobs.txt create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/results.html create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/results.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/results.xunit create mode 100644 reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/tools.yml diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md index bbff74bf2..797182051 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 Nov 11 06:27:09 2024Mon Nov 04 06:27:38 2024
1ToolsetMon Nov 11 18:31:52 2024Mon Nov 04 18:33:04 2024
2ToolsetTue Nov 12 06:26:56 2024Tue Nov 05 06:28:13 2024
3ToolsetTue Nov 05 18:32:47 2024Tue Oct 29 18:34:14 2024
4ToolsetWed Nov 06 06:27:59 2024Wed Oct 23 06:27:36 2024
5ToolsetWed Nov 06 18:32:51 2024Wed Oct 30 18:34:11 2024
6ToolsetThu Nov 07 06:26:50 2024Thu Oct 31 06:26:39 2024
7ToolsetThu Nov 07 18:38:42 2024Thu Oct 31 18:32:34 2024
8ToolsetFri Nov 08 06:28:01 2024Fri Nov 01 06:27:34 2024
9ToolsetFri Nov 08 18:33:31 2024Fri Nov 01 18:32:35 2024
10ToolsetSat Nov 09 06:25:38 2024Sat Nov 02 06:24:54 2024
11ToolsetSat Nov 09 18:31:23 2024Sat Nov 02 18:31:34 2024
12ToolsetSun Nov 10 06:26:10 2024Sun Nov 03 06:27:59 2024
13ToolsetSun Nov 10 18:30:47 2024Sun Nov 03 18:32:07 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Nov 11 06:27:09 2024Mon Nov 04 06:27:38 2024
1ToolsetMon Nov 11 18:31:52 2024Mon Nov 04 18:33:04 2024
2ToolsetTue Nov 12 06:26:56 2024Tue Nov 05 06:28:13 2024
3ToolsetTue Nov 12 18:33:46 2024Tue Nov 05 18:32:47 2024
4ToolsetWed Nov 06 06:27:59 2024Wed Oct 23 06:27:36 2024
5ToolsetWed Nov 06 18:32:51 2024Wed Oct 30 18:34:11 2024
6ToolsetThu Nov 07 06:26:50 2024Thu Oct 31 06:26:39 2024
7ToolsetThu Nov 07 18:38:42 2024Thu Oct 31 18:32:34 2024
8ToolsetFri Nov 08 06:28:01 2024Fri Nov 01 06:27:34 2024
9ToolsetFri Nov 08 18:33:31 2024Fri Nov 01 18:32:35 2024
10ToolsetSat Nov 09 06:25:38 2024Sat Nov 02 06:24:54 2024
11ToolsetSat Nov 09 18:31:23 2024Sat Nov 02 18:31:34 2024
12ToolsetSun Nov 10 06:26:10 2024Sun Nov 03 06:27:59 2024
13ToolsetSun Nov 10 18:30:47 2024Sun Nov 03 18:32:07 2024
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json index cdf3756d8..e0ef4c57b 100644 --- a/reports/anvil-edge/tool-tests/chunks.json +++ b/reports/anvil-edge/tool-tests/chunks.json @@ -14,11 +14,11 @@ "date2": "Tue Nov 05 06:28:13 2024" }, "3": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-05-18-17-1/results.html", - "date1": "Tue Nov 05 18:32:47 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-05-18-17-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-10-29-18-18-1/results.html", - "date2": "Tue Oct 29 18:34:14 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/results.html", + "date1": "Tue Nov 12 18:33:46 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-05-18-17-1/results.html", + "date2": "Tue Nov 05 18:32:47 2024" }, "4": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-06-06-12-1/results.html", diff --git a/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/chunk.json new file mode 100644 index 000000000..f38fad5c5 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/chunk.json @@ -0,0 +1,7 @@ +{ + "3": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/results.html", + "date1": "Tue Nov 12 18:33:46 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/chunk.txt new file mode 100644 index 000000000..d0d4a0789 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/chunk.txt @@ -0,0 +1,25 @@ +-t racon --tool-version a199cd7ac344 +-t deeptools_compute_gc_bias --tool-version 2bc10a9ca58b +-t fastq_manipulation --tool-version 5b87038565bb +-t ncbi_acc_download --tool-version 1c58de56d587 +-t mummer_show_coords --tool-version 959c1f8dae95 +-t poretools_squiggle --tool-version 34553d0caa5e +-t kallisto_quant --tool-version 60f888039fb2 +-t bamtools --tool-version 4d343c1f606b +-t samtools_idxstats --tool-version 7a6034296ae9 +-t samtools_idxstats --tool-version 7def34e6cf4d +-t music_inspect_eset --tool-version 2fed32b5aa02 +-t music_inspect_eset --tool-version 7705cc75ac18 +-t raceid_inspectclusters --tool-version 2b0d3e2f402a +-t raceid_inspectclusters --tool-version 41f34e925bd5 +-t scater_plot_pca --tool-version 46fc6751d746 +-t scater_plot_pca --tool-version c99ba278dfa9 +-t scanpy_filter_cells --tool-version 4c42e5d8cb7c +-t scanpy_filter_cells --tool-version ba64b91ed2b9 +-t column_maker --tool-version 02026300aa45 +-t column_order_header_sort --tool-version 6ae9724caf4d +-t sniffles --tool-version 93c4b04a0769 +-t bcftools_concat --tool-version d40d4bf05718 +-t bcftools_annotate --tool-version 403553ae19f6 +-t vcffixup --tool-version 11f62f071125 +-t vcftools_annotate --tool-version 57a6550df582 diff --git a/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/029e02c70d71eef6.json b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/029e02c70d71eef6.json new file mode 100644 index 000000000..0334fdca4 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/029e02c70d71eef6.json @@ -0,0 +1,99 @@ +{ + "model_class": "Job", + "id": "029e02c70d71eef6", + "history_id": "aff48f2f86cebb71", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0", + "state": "error", + "exit_code": 1, + "create_time": "2024-11-12T18:50:46.427135", + "update_time": "2024-11-12T18:51:04.046592", + "galaxy_version": "24.1", + "external_id": "gxy-swbm2", + "handler": null, + "job_runner_name": null, + "command_line": "echo 'CP011064,CP0XXXXX,CP021680' | sed -r 's/(\\,|__cn__)/\\n/g' | grep -v \"^[ \\t]*$\" > accessions && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'fasta' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", + "user_email": "tests@fake.org", + "command_version": "", + "params": { + "__input_ext": "\"data\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "ignore_failed": "\"0\"", + "range": null, + "molecule": "{\"__current_case__\": 0, \"format\": \"fasta\", \"select\": \"nucleotide\"}", + "query_source": "{\"__current_case__\": 1, \"accession_list\": \"CP011064,CP0XXXXX,CP021680\", \"select\": \"accession_list\"}" + }, + "inputs": {}, + "outputs": { + "error_log": { + "id": "13425de6bbb40c0b", + "src": "hda", + "uuid": "aa51de1d-551c-4c0c-8b0f-99d13243198f" + }, + "__new_primary_file_output|CP011064__": { + "id": "88235e930e2cb894", + "src": "hda", + "uuid": "6859ef04-6e9c-4061-a421-7ff923f423af" + } + }, + "copied_from_job_id": null, + "output_collections": { + "output": { + "src": "hdca", + "id": "919ed9e80b102f05" + } + }, + "tool_stdout": "NCBI Entrez returned error code 400, are ID(s) CP0XXXXX valid?\n", + "tool_stderr": "Failed to download file with id CP0XXXXX from NCBI\n", + "job_stdout": "", + "job_stderr": "", + "stdout": "NCBI Entrez returned error code 400, are ID(s) CP0XXXXX valid?\n", + "stderr": "Failed to download file with id CP0XXXXX from NCBI\n", + "job_messages": [ + { + "code_desc": "", + "desc": "Fatal error: Exit code 1 ()", + "error_level": 3, + "exit_code": 1, + "type": "exit_code" + } + ], + "dependencies": [], + "job_metrics": [ + { + "title": "Job Runtime (Wall Clock)", + "value": "4 seconds", + "plugin": "core", + "name": "runtime_seconds", + "raw_value": "4.0000000" + }, + { + "title": "Job End Time", + "value": "2024-11-12 18:50:51", + "plugin": "core", + "name": "end_epoch", + "raw_value": "1731437451.0000000" + }, + { + "title": "Job Start Time", + "value": "2024-11-12 18:50:47", + "plugin": "core", + "name": "start_epoch", + "raw_value": "1731437447.0000000" + }, + { + "title": "Memory Allocated (MB)", + "value": "4080", + "plugin": "core", + "name": "galaxy_memory_mb", + "raw_value": "4080.0000000" + }, + { + "title": "Cores Allocated", + "value": "1", + "plugin": "core", + "name": "galaxy_slots", + "raw_value": "1.0000000" + } + ] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/131fdfbf0346cb1a.json b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/131fdfbf0346cb1a.json new file mode 100644 index 000000000..e779c75d8 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/131fdfbf0346cb1a.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "131fdfbf0346cb1a", + "history_id": "aff48f2f86cebb71", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-11-12T19:07:16.762776", + "update_time": "2024-11-12T19:07:28.176788", + "galaxy_version": "24.1", + "external_id": "gxy-856zs", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/119/registry.xml' '/galaxy/server/database/jobs_directory/000/119/upload_params.json' '153:/galaxy/server/database/objects/8/b/7/dataset_8b7fe276-8679-4951-937e-81609e469184_files:/galaxy/server/database/objects/8/b/7/dataset_8b7fe276-8679-4951-937e-81609e469184.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_sre65yyk\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"EMTABesethealthy.subset.rds\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_vxhejdzk\", \"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": "3afdcc1316e79fd7", + "src": "hda", + "uuid": "8b7fe276-8679-4951-937e-81609e469184" + } + }, + "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-24-11-12-18-17-1/errors/22517353a62337da.json b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/22517353a62337da.json new file mode 100644 index 000000000..2275a0daa --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/22517353a62337da.json @@ -0,0 +1,47 @@ +{ + "model_class": "Job", + "id": "22517353a62337da", + "history_id": "aff48f2f86cebb71", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0", + "state": "error", + "exit_code": null, + "create_time": "2024-11-12T19:32:39.003959", + "update_time": "2024-11-12T19:32:51.328111", + "galaxy_version": "24.1", + "external_id": "gxy-rcxxp", + "handler": null, + "job_runner_name": null, + "command_line": "vcffixup '/galaxy/server/database/objects/4/3/8/dataset_4388fc55-f87a-4119-a927-a2b62cec447f.dat' > '/galaxy/server/database/objects/5/0/7/dataset_5074dd1a-a586-4e2b-a282-669b9f6fe7eb.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"vcf\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"" + }, + "inputs": { + "input1": { + "id": "1e5b4154869d2527", + "src": "hda", + "uuid": "4388fc55-f87a-4119-a927-a2b62cec447f" + } + }, + "outputs": { + "out_file1": { + "id": "60b15a076fb33d1f", + "src": "hda", + "uuid": "5074dd1a-a586-4e2b-a282-669b9f6fe7eb" + } + }, + "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-24-11-12-18-17-1/errors/2e4c4b2409f06dfd.json b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/2e4c4b2409f06dfd.json new file mode 100644 index 000000000..7410d91c1 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/2e4c4b2409f06dfd.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "2e4c4b2409f06dfd", + "history_id": "aff48f2f86cebb71", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-11-12T18:44:48.697434", + "update_time": "2024-11-12T18:45:00.519130", + "galaxy_version": "24.1", + "external_id": "gxy-dl2rp", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/38/registry.xml' '/galaxy/server/database/jobs_directory/000/38/upload_params.json' '38:/galaxy/server/database/objects/f/a/d/dataset_fadefed9-046c-4ace-9377-f4481496eec8_files:/galaxy/server/database/objects/f/a/d/dataset_fadefed9-046c-4ace-9377-f4481496eec8.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_evj6z0s6\"", + "files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"sanger_full_range_original_sanger.fastqsanger\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_u66b9_c9\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "2e4c4b2409f06dfd", + "src": "hda", + "uuid": "fadefed9-046c-4ace-9377-f4481496eec8" + } + }, + "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-24-11-12-18-17-1/errors/300354dbb5b5c093.json b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/300354dbb5b5c093.json new file mode 100644 index 000000000..fad003764 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/300354dbb5b5c093.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "300354dbb5b5c093", + "history_id": "aff48f2f86cebb71", + "tool_id": 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a/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/5e4710b2acc93880.json b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/5e4710b2acc93880.json new file mode 100644 index 000000000..a628fdd3d --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/5e4710b2acc93880.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "5e4710b2acc93880", + "history_id": "aff48f2f86cebb71", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-11-12T19:24:05.884320", + "update_time": "2024-11-12T19:24:16.737712", + "galaxy_version": "24.1", + "external_id": "gxy-vvv4s", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/169/registry.xml' '/galaxy/server/database/jobs_directory/000/169/upload_params.json' 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toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4 +7d2d2c51748ad56f ok 2024-11-12T19:26:45.504650 upload1 +0f16dae587208407 ok 2024-11-12T19:26:45.466502 upload1 +da121350c2eb0bb0 ok 2024-11-12T19:26:43.352409 upload1 +370edcd9ecc25e2e ok 2024-11-12T19:26:17.936656 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4 +f10ce5c4ebdb9e0b ok 2024-11-12T19:26:02.264205 upload1 +f513c7a4175656ca ok 2024-11-12T19:26:02.233893 upload1 +c1c7d45bbc4afcf9 ok 2024-11-12T19:25:40.449493 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4 +d89e5e5bf056cb9a ok 2024-11-12T19:25:24.865014 upload1 +6fb380a08528e60e ok 2024-11-12T19:25:24.792783 upload1 +b9e75b84021da46a ok 2024-11-12T19:25:02.036291 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4 +2289b72a1e64220c ok 2024-11-12T19:24:47.401810 upload1 +628f5fd9270d3535 ok 2024-11-12T19:24:47.317268 upload1 +8b3795696a00ae63 ok 2024-11-12T19:24:25.431938 upload1 +5e4710b2acc93880 error 2024-11-12T19:24:16.737712 upload1 +5652bfd859442e3e ok 2024-11-12T19:24:04.943981 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4 +a1b0ad5fe9f7ced6 ok 2024-11-12T19:23:48.286930 upload1 +95a958996bd8dcdb ok 2024-11-12T19:23:48.222589 upload1 +599f5eb0ef7cf54f ok 2024-11-12T19:23:25.472497 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4 +5f70adee03232999 ok 2024-11-12T19:23:01.544289 upload1 +bcc16562bd9918a7 ok 2024-11-12T19:23:00.625515 upload1 +bef9ef82cea6186b ok 2024-11-12T19:22:37.976207 toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0 +5cd3c25977cb89aa ok 2024-11-12T19:22:22.725134 upload1 +2d1ef22cada24364 ok 2024-11-12T19:22:00.475785 toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0 +1f3a1712d563f8a4 ok 2024-11-12T19:21:46.268726 upload1 +c6e0259b7027cf38 ok 2024-11-12T19:21:24.205776 toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0 +c032dc34d0e4e174 ok 2024-11-12T19:21:10.140692 upload1 +a9f5e69b88d408bc ok 2024-11-12T19:20:47.853161 toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0 +95405c34fd777349 ok 2024-11-12T19:20:33.898870 upload1 +3afdcc1316e79fd7 ok 2024-11-12T19:20:11.838903 toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0 +f7b695b1a284d214 ok 2024-11-12T19:19:56.507391 upload1 +d7a8c3e6bbd352d3 ok 2024-11-12T19:19:34.223322 toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0 +f9bbda75456259f7 ok 2024-11-12T19:19:15.900256 upload1 +ac499b98968b8cd4 ok 2024-11-12T19:18:52.886800 toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1 +9624d7910c3ae38a ok 2024-11-12T19:18:31.727745 upload1 +8c9efe74e55d3ced ok 2024-11-12T19:18:06.327592 toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.22.0 +a11164a95b2912ea ok 2024-11-12T19:17:41.136713 upload1 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toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy3 +1af93ef506a428b3 ok 2024-11-12T19:13:14.345149 upload1 +6a63091d0643274c ok 2024-11-12T19:12:51.380942 toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy3 +7f2ba4a96f863635 ok 2024-11-12T19:12:33.154916 upload1 +78df6a7e938194e0 ok 2024-11-12T19:12:11.052924 toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy3 +c92934e7acb83a07 ok 2024-11-12T19:11:51.713144 upload1 +f6b8ce2d03f988e7 ok 2024-11-12T19:11:29.696864 toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy3 +acdc23922eb4803c ok 2024-11-12T19:11:10.242237 upload1 +04593e2af642af4f ok 2024-11-12T19:10:43.223193 toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy3 +f7b94f0417131e60 ok 2024-11-12T19:10:23.897822 upload1 +157884e8db7f64e1 ok 2024-11-12T19:10:01.816247 toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy3 +398f31ab4e322c65 ok 2024-11-12T19:09:44.515712 upload1 +86e354b1a2664edb ok 2024-11-12T19:09:22.335659 toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy3 +50a349429066c0ac ok 2024-11-12T19:08:29.684961 upload1 +aa1970df5d90212f ok 2024-11-12T19:08:07.502493 toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy0 +565c15e90e40f485 ok 2024-11-12T19:07:48.122815 upload1 +131fdfbf0346cb1a error 2024-11-12T19:07:28.176788 upload1 +43dd47fc03a922dc ok 2024-11-12T19:07:15.686466 toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy0 +bd5d21d926d0e24f ok 2024-11-12T19:06:56.533637 upload1 +680541cf772f940a ok 2024-11-12T19:06:33.249256 toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy0 +f01e3d765cb45d79 ok 2024-11-12T19:06:14.168332 upload1 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2024-11-12T18:59:00.549374 upload1 +6e1c2e6968a87ac8 ok 2024-11-12T18:58:47.746222 toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1 +067bccd0f482ca57 ok 2024-11-12T18:58:31.896695 upload1 +0f677018cfea6707 ok 2024-11-12T18:58:31.821209 upload1 +6c955d50c7f34b11 ok 2024-11-12T18:58:30.806741 upload1 +56140019ab5a4fa3 ok 2024-11-12T18:58:05.168930 upload1 +c35a46ca1a22d289 ok 2024-11-12T18:58:05.130004 upload1 +8c6a9b7b4f005250 ok 2024-11-12T18:57:42.347220 toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1 +f3872516fc2aa29e ok 2024-11-12T18:57:28.110385 upload1 +b0cd527236ef4d8d ok 2024-11-12T18:57:28.050256 upload1 +2d95868d81555422 ok 2024-11-12T18:57:26.612243 upload1 +58144eee3514d507 ok 2024-11-12T18:57:00.372226 toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1 +bca3f0b433766ba2 ok 2024-11-12T18:56:46.437191 upload1 +3ea0ea787be2429e ok 2024-11-12T18:56:46.374544 upload1 +d5840e1b86480382 ok 2024-11-12T18:56:34.629406 upload1 +736d866f9311b390 ok 2024-11-12T18:56:34.611960 upload1 +9a957b6f1413b47b error 2024-11-12T18:56:24.973370 upload1 +e8b7d0422a3a8c75 ok 2024-11-12T18:56:12.254112 toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1 +79589384ffcafaa1 ok 2024-11-12T18:55:57.755072 upload1 +13425de6bbb40c0b ok 2024-11-12T18:55:57.545132 upload1 +88235e930e2cb894 ok 2024-11-12T18:55:57.510306 upload1 +936794faaa4e63cc ok 2024-11-12T18:55:29.358230 toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1 +9b585f26972e9c6e ok 2024-11-12T18:55:10.093245 upload1 +45a325aec3f9dbbb ok 2024-11-12T18:55:10.074553 upload1 +ae57a293c06b5b11 ok 2024-11-12T18:55:08.964352 upload1 +84c6a33fe5819f58 ok 2024-11-12T18:54:41.631266 toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1 +7464bd32972f4fb8 ok 2024-11-12T18:54:15.441133 upload1 +a91eb06094fb8638 ok 2024-11-12T18:53:53.152307 toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1 +4539719266c0e22d ok 2024-11-12T18:52:57.448011 upload1 +eee892f340a734c7 error 2024-11-12T18:52:35.029337 toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3 +19fc2c8095a84081 ok 2024-11-12T18:52:22.632881 upload1 +0a73fa7e75ba2878 ok 2024-11-12T18:52:00.405536 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +932643a400860814 ok 2024-11-12T18:51:42.423746 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +6eb7d1a976e3e08a ok 2024-11-12T18:51:25.225070 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +029e02c70d71eef6 error 2024-11-12T18:51:04.046592 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 +a0e3c015f452297d ok 2024-11-12T18:50:45.840499 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0 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2024-11-12T18:43:58.578861 upload1 +8f860481d6d25c66 ok 2024-11-12T18:43:37.352181 toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5 +16943600904ec72a ok 2024-11-12T18:43:22.360271 upload1 +534772d3377c9044 ok 2024-11-12T18:43:00.585525 toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5 +6b7e2b2d2f165b9e ok 2024-11-12T18:42:46.303192 upload1 +5c8a2a0609cd7daa ok 2024-11-12T18:42:24.341642 toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5 +6dd9c10378209a27 ok 2024-11-12T18:42:10.242148 upload1 +660613665eac52a8 ok 2024-11-12T18:41:48.973601 toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5 +9b9f22bd2de87785 ok 2024-11-12T18:41:35.784952 upload1 +afbab338e08c854f ok 2024-11-12T18:41:14.797326 toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5 +facebdcaf2e32703 ok 2024-11-12T18:41:00.746199 upload1 +a66057b922f6c74e ok 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mode 100644 index 000000000..5d43446d1 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/results.html @@ -0,0 +1,291 @@ + + + + + + + Test Results (powered by Planemo) + + + + + + + + + + +
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+ + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/results.json b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/results.json new file mode 100644 index 000000000..3bacad43d --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 96, "errors": 12, "failures": 4, "skips": 0}, "tests": [{"id": "bamtools/2.5.2+galaxy2-0", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.5.2+galaxy2", "test_index": 0, "time_seconds": 56.79121971130371, "inputs": {"input_bams": {"src": "hda", "id": "f6b8ce2d03f988e7"}, "analysis_type|format_type|reference_source|ref_file": {"src": "hda", "id": "c92934e7acb83a07"}, "analysis_type|format_type|reference_source|reference_source_selector": "history", "analysis_type|format_type|mapqual": true, "analysis_type|format_type|format_type_selector": "pileup", "analysis_type|analysis_type_selector": "convert"}, "job": {"model_class": "Job", "id": "e0c616b41a208ee0", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T18:59:39.859687", "update_time": "2024-11-12T18:59:58.224893", "galaxy_version": "24.1", "external_id": "gxy-wtwjd", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/f/e/c/dataset_fecac5cf-8aa7-47d9-9815-b4688e36d059.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/f/3/1/metadata_f316d227-ba07-429b-a47a-74c906d17ba0.dat' localbam.bam.bai && ln -s '/galaxy/server/database/objects/7/c/1/dataset_7c1c97e0-835c-4663-b921-8c42f919bd1e.dat' 'localref.fa' && samtools faidx 'localref.fa' 2>&1 || echo 'Error running samtools faidx for bamtools convert' >&2 && bamtools convert -format pileup -mapqual -fasta 'localref.fa' -out '/galaxy/server/database/objects/b/2/b/dataset_b2b35e57-000d-4413-9ad6-165e2891f7db.dat' -in localbam.bam", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"convert\", \"format_type\": {\"__current_case__\": 5, \"format_type_selector\": \"pileup\", \"mapqual\": true, \"reference_source\": {\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 130, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}}}"}, "inputs": {"input_bams": {"id": "f6b8ce2d03f988e7", "src": "hda", "uuid": "fecac5cf-8aa7-47d9-9815-b4688e36d059"}, "analysis_type|format_type|reference_source|ref_file": {"id": "c92934e7acb83a07", "src": "hda", "uuid": "7c1c97e0-835c-4663-b921-8c42f919bd1e"}}, "outputs": {"out_file1": {"id": "78df6a7e938194e0", "src": "hda", "uuid": "b2b35e57-000d-4413-9ad6-165e2891f7db"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Pileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Pileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\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": "2024-11-12 18:59:45", "plugin": "core", "name": "end_epoch", "raw_value": "1731437985.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 18:59:45", "plugin": "core", "name": "start_epoch", "raw_value": "1731437985.0000000"}, {"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": "bamtools/2.5.2+galaxy2-1", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.5.2+galaxy2", "test_index": 1, "time_seconds": 37.60291361808777, "inputs": {"input_bams": {"src": "hda", "id": "7f2ba4a96f863635"}, "analysis_type|analysis_type_selector": "count"}, "job": {"model_class": "Job", "id": "cd8a2c7c5538f3b6", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:00:20.960449", "update_time": "2024-11-12T19:00:35.859429", "galaxy_version": "24.1", "external_id": "gxy-hhp69", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/7/9/0/dataset_7900616d-6975-4c25-a814-4ddd2ecdcdf1.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/8/2/6/metadata_8261e336-e74a-4a9a-ba0a-f4c8e9eb92ec.dat' localbam.bam.bai && bamtools count > '/galaxy/server/database/objects/0/6/7/dataset_067dcc86-5637-4293-a1bf-ffe6144a488b.dat' -in localbam.bam", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 1, \"analysis_type_selector\": \"count\"}"}, "inputs": {"input_bams": {"id": "7f2ba4a96f863635", "src": "hda", "uuid": "7900616d-6975-4c25-a814-4ddd2ecdcdf1"}}, "outputs": {"out_file1": {"id": "6a63091d0643274c", "src": "hda", "uuid": "067dcc86-5637-4293-a1bf-ffe6144a488b"}}, "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": "2024-11-12 19:00:22", "plugin": "core", "name": "end_epoch", "raw_value": "1731438022.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:00:22", "plugin": "core", "name": "start_epoch", "raw_value": "1731438022.0000000"}, {"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": "bamtools/2.5.2+galaxy2-2", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.5.2+galaxy2", "test_index": 2, "time_seconds": 37.27437901496887, "inputs": {"input_bams": {"src": "hda", "id": "1af93ef506a428b3"}, "analysis_type|analysis_type_selector": "coverage"}, "job": {"model_class": "Job", "id": "2d3b334463434585", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:00:58.327243", "update_time": "2024-11-12T19:01:12.991485", "galaxy_version": "24.1", "external_id": "gxy-hqtnp", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/2/1/9/dataset_219c8688-4b39-473e-8cab-71968f09b058.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/b/9/f/metadata_b9f92f9b-6501-476a-9d1c-7cec6a916024.dat' localbam.bam.bai && bamtools coverage -out '/galaxy/server/database/objects/1/f/3/dataset_1f3ac34d-3e12-4fb1-a9da-a753e4b0dcc7.dat' -in localbam.bam", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 2, \"analysis_type_selector\": \"coverage\"}"}, "inputs": {"input_bams": {"id": "1af93ef506a428b3", "src": "hda", "uuid": "219c8688-4b39-473e-8cab-71968f09b058"}}, "outputs": {"out_file1": {"id": "b9dded51bc383d46", "src": "hda", "uuid": "1f3ac34d-3e12-4fb1-a9da-a753e4b0dcc7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Pileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Pileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\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": "2024-11-12 19:00:59", "plugin": "core", "name": "end_epoch", "raw_value": "1731438059.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:00:59", "plugin": "core", "name": "start_epoch", "raw_value": "1731438059.0000000"}, {"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": "bamtools/2.5.2+galaxy2-3", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.5.2+galaxy2", "test_index": 3, "time_seconds": 35.974133014678955, "inputs": {"input_bams": {"src": "hda", "id": "1830207951950a81"}, "analysis_type|analysis_type_selector": "header"}, "job": {"model_class": "Job", "id": "69df69147327c7f2", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:01:35.625973", "update_time": "2024-11-12T19:01:49.269747", "galaxy_version": "24.1", "external_id": "gxy-nzw2q", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/a/5/c/dataset_a5c19f61-c157-44f9-a3a7-c8920003bd27.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/0/9/5/metadata_095a50b6-f057-407c-82ea-c48b808fbdd5.dat' localbam.bam.bai && bamtools header > '/galaxy/server/database/objects/8/e/5/dataset_8e56224f-44f2-463c-ab3f-1c317d792282.dat' -in localbam.bam", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "analysis_type": "{\"__current_case__\": 3, \"analysis_type_selector\": \"header\"}"}, "inputs": {"input_bams": {"id": "1830207951950a81", "src": "hda", "uuid": "a5c19f61-c157-44f9-a3a7-c8920003bd27"}}, "outputs": {"out_file1": {"id": "1043351839cd2063", "src": "hda", "uuid": "8e56224f-44f2-463c-ab3f-1c317d792282"}}, "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": "2024-11-12 19:01:37", "plugin": "core", "name": "end_epoch", "raw_value": "1731438097.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:01:37", "plugin": "core", "name": "start_epoch", "raw_value": "1731438097.0000000"}, {"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_annotate/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 41.55721688270569, "inputs": {"input_file": {"src": "hda", "id": "af23e27e6ea456bf"}, "sec_annofile|columns": "CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL", "sec_annofile|annofile|annotations": {"src": "hda", "id": "6f214e9224e87c39"}, "sec_annofile|annofile|header_file": {"src": "hda", "id": "0fb9ab45137f45e7"}, "sec_annofile|annofile|anno_fmt": "tab", "output_type": "v"}, "job": {"model_class": "Job", "id": "66593abfb0b70743", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:26:45.682308", "update_time": "2024-11-12T19:27:00.502915", "galaxy_version": "24.1", "external_id": "gxy-7k26q", "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/3/3/1/dataset_331f3232-3e09-48a1-befc-13b8fa4fdec3.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c '/galaxy/server/database/objects/c/9/5/dataset_c955d01d-d0c3-461c-bf1f-eadce490b077.dat' > annotations.tab.gz && tabix -s 1 -b 2 -e 2 annotations.tab.gz && bcftools annotate --columns 'CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL' --annotations 'annotations.tab.gz' --header-lines '/galaxy/server/database/objects/b/a/7/dataset_ba7be161-0fcf-456d-a76c-6db2643b4c05.dat' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/5/0/0/dataset_500a2e88-5231-41bf-9573-21ebbf7d59ae.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": "{\"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}", "sec_annotate": "{\"remove\": \"\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 2, \"anno_fmt\": \"tab\", \"annotations\": {\"values\": [{\"id\": 224, \"src\": \"hda\"}]}, \"header_file\": {\"values\": [{\"id\": 225, \"src\": \"hda\"}]}, \"header_lines\": null}, \"columns\": \"CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "af23e27e6ea456bf", "src": "hda", "uuid": "331f3232-3e09-48a1-befc-13b8fa4fdec3"}, "sec_annofile|annofile|annotations": {"id": "6f214e9224e87c39", "src": "hda", "uuid": "c955d01d-d0c3-461c-bf1f-eadce490b077"}, "sec_annofile|annofile|header_file": {"id": "0fb9ab45137f45e7", "src": "hda", "uuid": "ba7be161-0fcf-456d-a76c-6db2643b4c05"}}, "outputs": {"output_file": {"id": "3e3fea67174018aa", "src": "hda", "uuid": "500a2e88-5231-41bf-9573-21ebbf7d59ae"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-12 19:26:48", "plugin": "core", "name": "end_epoch", "raw_value": "1731439608.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:26:47", "plugin": "core", "name": "start_epoch", "raw_value": "1731439607.0000000"}, {"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_annotate/1.15.1+galaxy4-1", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 1, "time_seconds": 23.25907254219055, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_annotate/1.15.1+galaxy4-2", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 2, "time_seconds": 37.91918992996216, "inputs": {"input_file": {"src": "hda", "id": "23f1f39e97b30adb"}, "sec_annofile|columns": "STR,ID,QUAL,FILTER", "sec_annofile|annofile|annotations": {"src": "hda", "id": "76ef864170ed0298"}, "sec_annofile|annofile|anno_fmt": "vcf", "output_type": "v"}, "job": {"model_class": "Job", "id": "6867bd8d18961a91", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:27:46.383042", "update_time": "2024-11-12T19:28:01.830034", "galaxy_version": "24.1", "external_id": "gxy-ff975", "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/e/3/dataset_6e371360-8cc8-4a8e-a948-2be979fdb173.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c '/galaxy/server/database/objects/4/3/3/dataset_43389552-baa2-4f6c-a331-59772507b4a1.dat' > annotations.vcf.gz && bcftools index annotations.vcf.gz && bcftools annotate --columns 'STR,ID,QUAL,FILTER' --annotations 'annotations.vcf.gz' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/8/9/1/dataset_891ec808-5972-4272-a4a4-a4ed5d268b20.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": "{\"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}", "sec_annotate": "{\"remove\": \"\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 1, \"anno_fmt\": \"vcf\", \"annotations\": {\"values\": [{\"id\": 231, \"src\": \"hda\"}]}}, \"columns\": \"STR,ID,QUAL,FILTER\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "23f1f39e97b30adb", "src": "hda", "uuid": "6e371360-8cc8-4a8e-a948-2be979fdb173"}, "sec_annofile|annofile|annotations": {"id": "76ef864170ed0298", "src": "hda", "uuid": "43389552-baa2-4f6c-a331-59772507b4a1"}}, "outputs": {"output_file": {"id": "c51c27faee9bc662", "src": "hda", "uuid": "891ec808-5972-4272-a4a4-a4ed5d268b20"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-12 19:27:49", "plugin": "core", "name": "end_epoch", "raw_value": "1731439669.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:27:48", "plugin": "core", "name": "start_epoch", "raw_value": "1731439668.0000000"}, {"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_annotate/1.15.1+galaxy4-3", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 3, "time_seconds": 36.279430866241455, "inputs": {"input_file": {"src": "hda", "id": "1413c47301458b01"}, "sec_annofile|columns": "STR,ID,QUAL,FILTER", "sec_annofile|annofile|annotations": {"src": "hda", "id": "650d848d329ce717"}, "sec_annofile|annofile|anno_fmt": "vcf", "output_type": "v"}, "job": {"model_class": "Job", "id": "c7fc36f1d6e16823", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:28:24.006127", "update_time": "2024-11-12T19:28:38.192553", "galaxy_version": "24.1", "external_id": "gxy-rgqzs", "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/1/0/dataset_c103061e-ff34-4cbb-a448-3fc648aa9d5c.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/d/8/a/dataset_d8a516d5-76d6-413e-93be-258c67b470d3.dat' annotations.bcf && ln -s '/galaxy/server/database/objects/_metadata_files/5/6/1/metadata_5613b83f-645d-4839-974c-6d08a49fefe3.dat' annotations.bcf.csi && bcftools annotate --columns 'STR,ID,QUAL,FILTER' --annotations 'annotations.bcf' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/0/3/2/dataset_0321849b-26a8-4e88-b534-7cacd007d130.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": "{\"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}", "sec_annotate": "{\"remove\": \"\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 1, \"anno_fmt\": \"vcf\", \"annotations\": {\"values\": [{\"id\": 234, \"src\": \"hda\"}]}}, \"columns\": \"STR,ID,QUAL,FILTER\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "1413c47301458b01", "src": "hda", "uuid": "c103061e-ff34-4cbb-a448-3fc648aa9d5c"}, "sec_annofile|annofile|annotations": {"id": "650d848d329ce717", "src": "hda", "uuid": "d8a516d5-76d6-413e-93be-258c67b470d3"}}, "outputs": {"output_file": {"id": "d40d1b0bdbae9428", "src": "hda", "uuid": "0321849b-26a8-4e88-b534-7cacd007d130"}}, "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": "2024-11-12 19:28:25", "plugin": "core", "name": "end_epoch", "raw_value": "1731439705.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:28:25", "plugin": "core", "name": "start_epoch", "raw_value": "1731439705.0000000"}, {"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_annotate/1.15.1+galaxy4-4", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 4, "time_seconds": 36.57880687713623, "inputs": {"input_file": {"src": "hda", "id": "341ec292db9fcbaa"}, "sec_annofile|columns": "ID,QUAL,FILTER,INFO,FMT", "sec_annofile|annofile|annotations": {"src": "hda", "id": "0c95006ffd69aa99"}, "sec_annofile|annofile|anno_fmt": "vcf", "output_type": "v"}, "job": {"model_class": "Job", "id": "723660a468bc344b", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:29:00.356481", "update_time": "2024-11-12T19:29:14.633579", "galaxy_version": "24.1", "external_id": "gxy-fjj87", "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/b/b/dataset_6bbc015f-e861-42b1-8ff0-b4d3d11dfcf3.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c '/galaxy/server/database/objects/b/1/c/dataset_b1c0bb36-86d0-472d-bbd2-2f39d385eac7.dat' > annotations.vcf.gz && bcftools index annotations.vcf.gz && bcftools annotate --columns 'ID,QUAL,FILTER,INFO,FMT' --annotations 'annotations.vcf.gz' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/1/3/0/dataset_13025467-fdd4-4244-a59e-64249f2f43cb.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": "{\"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}", "sec_annotate": "{\"remove\": \"\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 1, \"anno_fmt\": \"vcf\", \"annotations\": {\"values\": [{\"id\": 237, \"src\": \"hda\"}]}}, \"columns\": \"ID,QUAL,FILTER,INFO,FMT\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "341ec292db9fcbaa", "src": "hda", "uuid": "6bbc015f-e861-42b1-8ff0-b4d3d11dfcf3"}, "sec_annofile|annofile|annotations": {"id": "0c95006ffd69aa99", "src": "hda", "uuid": "b1c0bb36-86d0-472d-bbd2-2f39d385eac7"}}, "outputs": {"output_file": {"id": "ca344e7788a91480", "src": "hda", "uuid": "13025467-fdd4-4244-a59e-64249f2f43cb"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-12 19:29:03", "plugin": "core", "name": "end_epoch", "raw_value": "1731439743.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:29:02", "plugin": "core", "name": "start_epoch", "raw_value": "1731439742.0000000"}, {"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_annotate/1.15.1+galaxy4-5", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 5, "time_seconds": 37.62701392173767, "inputs": {"input_file": {"src": "hda", "id": "45c8ecef28a51f7e"}, "sec_annofile|columns": "ID,QUAL,FILTER,INFO,FMT", "sec_annofile|annofile|annotations": {"src": "hda", "id": "6ff25b1fee2869cc"}, "sec_annofile|annofile|anno_fmt": "vcf", "sec_restrict|samples": "A", "output_type": "v"}, "job": {"model_class": "Job", "id": "6521c6a01a09c7e3", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:29:37.962283", "update_time": "2024-11-12T19:29:52.359901", "galaxy_version": "24.1", "external_id": "gxy-c79rk", "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/c/5/dataset_4c542729-745d-4da5-937b-863418e2d930.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c '/galaxy/server/database/objects/9/4/0/dataset_94051840-f069-443f-970c-13a6405d503b.dat' > annotations.vcf.gz && bcftools index annotations.vcf.gz && bcftools annotate --columns 'ID,QUAL,FILTER,INFO,FMT' --annotations 'annotations.vcf.gz' --samples 'A' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/1/a/1/dataset_1a125f4e-00e4-4cf8-aef4-176e70e331f5.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": "{\"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"A\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 1, \"anno_fmt\": \"vcf\", \"annotations\": {\"values\": [{\"id\": 240, \"src\": \"hda\"}]}}, \"columns\": \"ID,QUAL,FILTER,INFO,FMT\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "45c8ecef28a51f7e", "src": "hda", "uuid": "4c542729-745d-4da5-937b-863418e2d930"}, "sec_annofile|annofile|annotations": {"id": "6ff25b1fee2869cc", "src": "hda", "uuid": "94051840-f069-443f-970c-13a6405d503b"}}, "outputs": {"output_file": {"id": "05f703c4fb641262", "src": "hda", "uuid": "1a125f4e-00e4-4cf8-aef4-176e70e331f5"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-12 19:29:40", "plugin": "core", "name": "end_epoch", "raw_value": "1731439780.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:29:39", "plugin": "core", "name": "start_epoch", "raw_value": "1731439779.0000000"}, {"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_annotate/1.15.1+galaxy4-6", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 6, "time_seconds": 37.095030784606934, "inputs": {"input_file": {"src": "hda", "id": "4232728db0548dfc"}, "sec_annofile|annofile|anno_fmt": "none", "sec_annotate|remove": "ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL", "output_type": "v"}, "job": {"model_class": "Job", "id": "1fd45311be778b92", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:30:14.443174", "update_time": "2024-11-12T19:30:29.429755", "galaxy_version": "24.1", "external_id": "gxy-rnl9j", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/6/7/dataset_f67cd30b-260e-4aa4-aecf-5d5387bada2d.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools annotate --remove 'ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/2/6/7/dataset_267849a5-2534-4fe6-b8e9-ab269c25835c.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": "{\"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}", "sec_annotate": "{\"remove\": \"ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 0, \"anno_fmt\": \"none\"}, \"columns\": \"\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "4232728db0548dfc", "src": "hda", "uuid": "f67cd30b-260e-4aa4-aecf-5d5387bada2d"}}, "outputs": {"output_file": {"id": "912b6c2109a28642", "src": "hda", "uuid": "267849a5-2534-4fe6-b8e9-ab269c25835c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-12 19:30:17", "plugin": "core", "name": "end_epoch", "raw_value": "1731439817.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:30:16", "plugin": "core", "name": "start_epoch", "raw_value": "1731439816.0000000"}, {"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_annotate/1.15.1+galaxy4-7", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 7, "time_seconds": 35.14488625526428, "inputs": {"input_file": {"src": "hda", "id": "8254e77320d6c7eb"}, "sec_annofile|annofile|anno_fmt": "none", "sec_annotate|remove": "FORMAT", "output_type": "v"}, "job": {"model_class": "Job", "id": "8282889456266094", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:30:50.969138", "update_time": "2024-11-12T19:31:04.792950", "galaxy_version": "24.1", "external_id": "gxy-fdsw6", "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/1/2/9/dataset_12936758-45ec-49de-8963-45a889fb4618.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools annotate --remove 'FORMAT' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/f/0/9/dataset_f09e4481-440b-471c-9d71-49766267b0d4.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": "{\"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}", "sec_annotate": "{\"remove\": \"FORMAT\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 0, \"anno_fmt\": \"none\"}, \"columns\": \"\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "8254e77320d6c7eb", "src": "hda", "uuid": "12936758-45ec-49de-8963-45a889fb4618"}}, "outputs": {"output_file": {"id": "aac1f99f2fed346c", "src": "hda", "uuid": "f09e4481-440b-471c-9d71-49766267b0d4"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-12 19:30:53", "plugin": "core", "name": "end_epoch", "raw_value": "1731439853.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:30:52", "plugin": "core", "name": "start_epoch", "raw_value": "1731439852.0000000"}, {"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_annotate/1.15.1+galaxy4-8", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 8, "time_seconds": 35.47008466720581, "inputs": {"input_file": {"src": "hda", "id": "a9b840775af87956"}, "sec_annofile|annofile|anno_fmt": "none", "sec_annotate|remove": "FORMAT", "sec_restrict|regions_overlap": "1", "output_type": "v"}, "job": {"model_class": "Job", "id": "26a32c328603d720", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:31:25.241726", "update_time": "2024-11-12T19:31:40.163416", "galaxy_version": "24.1", "external_id": "gxy-cf5rc", "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/d/7/f/dataset_d7f34e14-f7b7-466a-9065-cf05247d48c6.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools annotate --remove 'FORMAT' --regions-overlap 1 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/c/9/a/dataset_c9a39c25-faf6-4504-bcad-33b67a7b0039.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": "{\"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}", "sec_annotate": "{\"remove\": \"FORMAT\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 0, \"anno_fmt\": \"none\"}, \"columns\": \"\", \"mark_sites\": \"\", \"min_overlap\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "a9b840775af87956", "src": "hda", "uuid": "d7f34e14-f7b7-466a-9065-cf05247d48c6"}}, "outputs": {"output_file": {"id": "215392b7976ed56a", "src": "hda", "uuid": "c9a39c25-faf6-4504-bcad-33b67a7b0039"}}, "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": "2024-11-12 19:31:27", "plugin": "core", "name": "end_epoch", "raw_value": "1731439887.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:31:27", "plugin": "core", "name": "start_epoch", "raw_value": "1731439887.0000000"}, {"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_annotate/1.15.1+galaxy4-9", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.15.1+galaxy4", "test_index": 9, "time_seconds": 36.068262338638306, "inputs": {"input_file": {"src": "hda", "id": "6568beec409ebe42"}, "sec_annofile|annofile|anno_fmt": "none", "sec_annofile|min_overlap": "0.5", "sec_annotate|remove": "FORMAT", "output_type": "v"}, "job": {"model_class": "Job", "id": "5a0ab83107e1f125", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:32:01.335941", "update_time": "2024-11-12T19:32:16.364132", "galaxy_version": "24.1", "external_id": "gxy-w9lbd", "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/1/1/1/dataset_11177cad-4858-4e00-b703-1eeb65afbc53.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools annotate --min-overlap '0.5' --remove 'FORMAT' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/f/b/d/dataset_fbd98685-51e1-4eb7-b089-30b51c8707bd.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": "{\"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}", "sec_annotate": "{\"remove\": \"FORMAT\", \"rename_annots\": null, \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 0, \"anno_fmt\": \"none\"}, \"columns\": \"\", \"mark_sites\": \"\", \"min_overlap\": \"0.5\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "6568beec409ebe42", "src": "hda", "uuid": "11177cad-4858-4e00-b703-1eeb65afbc53"}}, "outputs": {"output_file": {"id": "07bcee9a4fb2da78", "src": "hda", "uuid": "fbd98685-51e1-4eb7-b089-30b51c8707bd"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-12 19:32:04", "plugin": "core", "name": "end_epoch", "raw_value": "1731439924.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:32:03", "plugin": "core", "name": "start_epoch", "raw_value": "1731439923.0000000"}, {"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_concat/1.15.1+galaxy4-0", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.15.1+galaxy4", "test_index": 0, "time_seconds": 46.582571268081665, "inputs": {"input_files": [{"src": "hda", "id": "2c15f43f6f08851e"}, {"src": "hda", "id": "22517353a62337da"}], "output_type": "v"}, "job": {"model_class": "Job", "id": "599f5eb0ef7cf54f", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:23:01.947531", "update_time": "2024-11-12T19:23:25.472497", "galaxy_version": "24.1", "external_id": "gxy-w8s5c", "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/d/3/9/dataset_d39221f2-f254-489c-b269-031aa6e5615d.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/a/b/9/dataset_ab9d5c38-2f6d-487f-a4e2-bba1d517e5ac.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools concat --allow-overlaps --min-PQ 30 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/c/8/b/dataset_c8b7d7f4-2002-4d47-a48a-05f0a8c6534f.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_default": "{\"compact_PS\": false, \"min_PQ\": \"30\", \"mode\": {\"__current_case__\": 1, \"ligate\": false, \"ligate_mode\": null, \"naive\": \"no\", \"overlaps\": {\"__current_case__\": 0, \"allow_overlaps\": \"yes\", \"rm_dups\": null}}}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null}"}, "inputs": {"input_files": {"id": "2c15f43f6f08851e", "src": "hda", "uuid": "d39221f2-f254-489c-b269-031aa6e5615d"}, "input_files1": {"id": "2c15f43f6f08851e", "src": "hda", "uuid": "d39221f2-f254-489c-b269-031aa6e5615d"}, "input_files2": {"id": "22517353a62337da", "src": "hda", "uuid": "ab9d5c38-2f6d-487f-a4e2-bba1d517e5ac"}}, "outputs": {"output_file": {"id": "1b46eaab6558b52e", "src": "hda", "uuid": "c8b7d7f4-2002-4d47-a48a-05f0a8c6534f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Checking the headers and starting positions of 2 files\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Checking the headers and starting positions of 2 files\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": "2024-11-12 19:23:12", "plugin": "core", "name": "end_epoch", "raw_value": "1731439392.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:23:11", "plugin": "core", "name": "start_epoch", "raw_value": "1731439391.0000000"}, {"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_concat/1.15.1+galaxy4-1", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.15.1+galaxy4", "test_index": 1, "time_seconds": 39.30913281440735, "inputs": {"input_files": [{"src": "hda", "id": "8c9b3cafb9e03de7"}, {"src": "hda", "id": "4cedbfaff565044e"}], "sec_default|mode|naive": "no", "output_type": "v"}, "job": {"model_class": "Job", "id": "5652bfd859442e3e", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:23:48.567394", "update_time": "2024-11-12T19:24:04.943981", "galaxy_version": "24.1", "external_id": "gxy-2znvz", "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/5/b/e/dataset_5be5993d-99fd-4296-8fb3-1ae67b9824c9.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/f/d/4/dataset_fd4204ca-e36d-46ed-93a4-fe4c02b54372.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools concat --allow-overlaps --min-PQ 30 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/e/0/6/dataset_e0686321-1ea5-4426-96d3-4eda51eed180.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_default": "{\"compact_PS\": false, \"min_PQ\": \"30\", \"mode\": {\"__current_case__\": 1, \"ligate\": false, \"ligate_mode\": null, \"naive\": \"no\", \"overlaps\": {\"__current_case__\": 0, \"allow_overlaps\": \"yes\", \"rm_dups\": null}}}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null}"}, "inputs": {"input_files": {"id": "8c9b3cafb9e03de7", "src": "hda", "uuid": "5be5993d-99fd-4296-8fb3-1ae67b9824c9"}, "input_files1": {"id": "8c9b3cafb9e03de7", "src": "hda", "uuid": "5be5993d-99fd-4296-8fb3-1ae67b9824c9"}, "input_files2": {"id": "4cedbfaff565044e", "src": "hda", "uuid": "fd4204ca-e36d-46ed-93a4-fe4c02b54372"}}, "outputs": {"output_file": {"id": "6d47b6b98bd893d8", "src": "hda", "uuid": "e0686321-1ea5-4426-96d3-4eda51eed180"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Checking the headers and starting positions of 2 files\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Checking the headers and starting positions of 2 files\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": "2024-11-12 19:23:52", "plugin": "core", "name": "end_epoch", "raw_value": "1731439432.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:23:51", "plugin": "core", "name": "start_epoch", "raw_value": "1731439431.0000000"}, {"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_concat/1.15.1+galaxy4-2", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.15.1+galaxy4", "test_index": 2, "time_seconds": 20.185490131378174, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_concat/1.15.1+galaxy4-3", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.15.1+galaxy4", "test_index": 3, "time_seconds": 36.75568699836731, "inputs": {"input_files": [{"src": "hda", "id": "26d703303a186e48"}, {"src": "hda", "id": "5f2233b5b560270c"}], "sec_default|mode|overlaps|rm_dups": "none", "sec_default|mode|overlaps|allow_overlaps": "yes", "output_type": "v"}, "job": {"model_class": "Job", "id": "b9e75b84021da46a", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:24:47.881854", "update_time": "2024-11-12T19:25:02.036291", "galaxy_version": "24.1", "external_id": "gxy-qs2p8", "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/5/b/3/dataset_5b39f5aa-c66c-4e97-9337-f2df4b0d0559.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/f/e/0/dataset_fe093081-80c6-4f50-8c9a-a35d0a13c5f2.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools concat --allow-overlaps --rm-dups none --min-PQ 30 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/f/6/4/dataset_f646c97d-6e2e-4b67-9161-6e7593347c96.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_default": "{\"compact_PS\": false, \"min_PQ\": \"30\", \"mode\": {\"__current_case__\": 1, \"ligate\": false, \"ligate_mode\": null, \"naive\": \"no\", \"overlaps\": {\"__current_case__\": 0, \"allow_overlaps\": \"yes\", \"rm_dups\": \"none\"}}}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null}"}, "inputs": {"input_files": {"id": "26d703303a186e48", "src": "hda", "uuid": "5b39f5aa-c66c-4e97-9337-f2df4b0d0559"}, "input_files1": {"id": "26d703303a186e48", "src": "hda", "uuid": "5b39f5aa-c66c-4e97-9337-f2df4b0d0559"}, "input_files2": {"id": "5f2233b5b560270c", "src": "hda", "uuid": "fe093081-80c6-4f50-8c9a-a35d0a13c5f2"}}, "outputs": {"output_file": {"id": "fe5f2ed4c0463843", "src": "hda", "uuid": "f646c97d-6e2e-4b67-9161-6e7593347c96"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Checking the headers and starting positions of 2 files\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Checking the headers and starting positions of 2 files\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": "2024-11-12 19:24:49", "plugin": "core", "name": "end_epoch", "raw_value": "1731439489.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:24:49", "plugin": "core", "name": "start_epoch", "raw_value": "1731439489.0000000"}, {"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_concat/1.15.1+galaxy4-4", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.15.1+galaxy4", "test_index": 4, "time_seconds": 38.2585027217865, "inputs": {"input_files": [{"src": "hda", "id": "8ee26c393cb3dfe7"}, {"src": "hda", "id": "f0defefeb3611578"}], "sec_restrict|regions_overlap": "1", "output_type": "v"}, "job": {"model_class": "Job", "id": "c1c7d45bbc4afcf9", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:25:25.266725", "update_time": "2024-11-12T19:25:40.449493", "galaxy_version": "24.1", "external_id": "gxy-fm8xw", "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/d/4/dataset_ad47e9db-2e7e-4721-a2ab-cd46d1c66a34.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/1/9/c/dataset_19c68235-ed3b-4da9-aca2-57dbff126436.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools concat --allow-overlaps --min-PQ 30 --regions-overlap 1 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/f/5/f/dataset_f5f034f3-835f-4a51-82ed-765e2981e8ec.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_default": "{\"compact_PS\": false, \"min_PQ\": \"30\", \"mode\": {\"__current_case__\": 1, \"ligate\": false, \"ligate_mode\": null, \"naive\": \"no\", \"overlaps\": {\"__current_case__\": 0, \"allow_overlaps\": \"yes\", \"rm_dups\": null}}}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": \"1\"}"}, "inputs": {"input_files": {"id": "8ee26c393cb3dfe7", "src": "hda", "uuid": "ad47e9db-2e7e-4721-a2ab-cd46d1c66a34"}, "input_files1": {"id": "8ee26c393cb3dfe7", "src": "hda", "uuid": "ad47e9db-2e7e-4721-a2ab-cd46d1c66a34"}, "input_files2": {"id": "f0defefeb3611578", "src": "hda", "uuid": "19c68235-ed3b-4da9-aca2-57dbff126436"}}, "outputs": {"output_file": {"id": "8afe68c0141b230b", "src": "hda", "uuid": "f5f034f3-835f-4a51-82ed-765e2981e8ec"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Checking the headers and starting positions of 2 files\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Checking the headers and starting positions of 2 files\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": "2024-11-12 19:25:27", "plugin": "core", "name": "end_epoch", "raw_value": "1731439527.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:25:27", "plugin": "core", "name": "start_epoch", "raw_value": "1731439527.0000000"}, {"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_concat/1.15.1+galaxy4-5", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.15.1+galaxy4", "test_index": 5, "time_seconds": 37.628992319107056, "inputs": {"input_files": [{"src": "hda", "id": "aacfcc007057ff9a"}, {"src": "hda", "id": "1a15c6acf0f51093"}], "sec_default|mode|overlaps|allow_overlaps": "no", "sec_default|mode|ligate": true, "sec_default|mode|ligate_mode": "--ligate-warn", "output_type": "v"}, "job": {"model_class": "Job", "id": "370edcd9ecc25e2e", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.15.1+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:26:02.607631", "update_time": "2024-11-12T19:26:17.936656", "galaxy_version": "24.1", "external_id": "gxy-8fbk8", "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/a/b/dataset_aabdc0a4-b813-49a3-ab6a-79ca54d48cc6.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/1/a/7/dataset_1a7e9bf7-d887-4515-a31f-983db85a19d8.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools concat --ligate --ligate-warn --min-PQ 30 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/5/7/4/dataset_5744a1b4-50ad-4b08-aa7e-1112a0acfe79.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_default": "{\"compact_PS\": false, \"min_PQ\": \"30\", \"mode\": {\"__current_case__\": 1, \"ligate\": true, \"ligate_mode\": \"--ligate-warn\", \"naive\": \"no\", \"overlaps\": {\"__current_case__\": 1, \"allow_overlaps\": \"no\"}}}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null}"}, "inputs": {"input_files": {"id": "aacfcc007057ff9a", "src": "hda", "uuid": "aabdc0a4-b813-49a3-ab6a-79ca54d48cc6"}, "input_files1": {"id": "aacfcc007057ff9a", "src": "hda", "uuid": "aabdc0a4-b813-49a3-ab6a-79ca54d48cc6"}, "input_files2": {"id": "1a15c6acf0f51093", "src": "hda", "uuid": "1a7e9bf7-d887-4515-a31f-983db85a19d8"}}, "outputs": {"output_file": {"id": "d7c614dc0dc2c6bd", "src": "hda", "uuid": "5744a1b4-50ad-4b08-aa7e-1112a0acfe79"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Checking the headers and starting positions of 2 files\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Checking the headers and starting positions of 2 files\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": "2024-11-12 19:26:05", "plugin": "core", "name": "end_epoch", "raw_value": "1731439565.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:26:04", "plugin": "core", "name": "start_epoch", "raw_value": "1731439564.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "column_order_header_sort/0.0.1-0", "has_data": true, "data": {"tool_id": "column_order_header_sort", "tool_version": "0.0.1", "test_index": 0, "time_seconds": 42.738149642944336, "inputs": {"input_tabular": {"src": "hda", "id": "ea816188a2b7fee0"}, "key_column": "1"}, "job": {"model_class": "Job", "id": "ac499b98968b8cd4", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:18:32.050856", "update_time": "2024-11-12T19:18:52.886800", "galaxy_version": "24.1", "external_id": "gxy-4x5wz", "handler": null, "job_runner_name": null, "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/6ae9724caf4d/column_order_header_sort/column_order_header_sort.py' '/galaxy/server/database/objects/b/5/c/dataset_b5ca7409-6d65-4980-8ae3-86ae67e96cad.dat' '/galaxy/server/database/objects/9/8/d/dataset_98d55e33-abb8-491f-9bed-c3567177604c.dat' '\t' '1'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "key_column": "\"1\""}, "inputs": {"input_tabular": {"id": "ea816188a2b7fee0", "src": "hda", "uuid": "b5ca7409-6d65-4980-8ae3-86ae67e96cad"}}, "outputs": {"output_tabular": {"id": "6d848fe4b8879795", "src": "hda", "uuid": "98d55e33-abb8-491f-9bed-c3567177604c"}}, "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": "2024-11-12 19:18:40", "plugin": "core", "name": "end_epoch", "raw_value": "1731439120.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:18:40", "plugin": "core", "name": "start_epoch", "raw_value": "1731439120.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output_tabular: different than expected, difference (using diff):\n( /tmp/tmp6i42p53bout_1.tabular v. /tmp/tmpqowvgy0oout_1.tabular )\n--- local_file\n+++ history_data\n@@ -1,4 +1,4 @@\n #KEY\ta\tb\tc\n one\t1-3\t1-1\t1-2\n two\t1-6\t1-4\t1-5\n-three\t1-9\t1-7\t1-8+three\t1-9\t1-7\t1-8\n"], "status": "failure"}}, {"id": "deeptools_compute_gc_bias/3.5.4+galaxy0-0", "has_data": true, "data": {"tool_id": "deeptools_compute_gc_bias", "tool_version": "3.5.4+galaxy0", "test_index": 0, "time_seconds": 61.94413423538208, "inputs": {"bamInput": {"src": "hda", "id": "1202ef0cf527ec74"}, "source|input1": {"src": "hda", "id": "4f483b3e97fc9303"}, "source|ref_source": "history", "effectiveGenomeSize|effectiveGenomeSize": "10050", "effectiveGenomeSize|effectiveGenomeSize_opt": "specific", "fragmentLength": "300", "region": "chr2L", "advancedOpt|sampleSize": "10", "advancedOpt|regionSize": "1", "advancedOpt|showAdvancedOpt": "yes", "image_format": "none"}, "job": {"model_class": "Job", "id": "0540b4f574011492", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.5.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T18:37:31.262354", "update_time": "2024-11-12T18:38:09.061694", "galaxy_version": "24.1", "external_id": "gxy-9s6nl", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/9/4/8/dataset_948a5f78-dc7c-4b96-92b6-53b9b0c86a3d.dat' local_bamInput.bam && ln -s '/galaxy/server/database/objects/_metadata_files/8/0/f/metadata_80f00aea-e20e-4dd5-a802-d1b8987515f0.dat' local_bamInput.bam.bai && computeGCBias --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bamfile local_bamInput.bam --GCbiasFrequenciesFile /galaxy/server/database/objects/8/e/7/dataset_8e799f2a-e4c9-4de7-93be-9f8f0ae4c15a.dat --fragmentLength 300 --genome /galaxy/server/database/objects/7/9/d/dataset_79d61f9d-60cb-4c38-a62f-871f868f12a7.dat --effectiveGenomeSize 10050 --region 'chr2L' --sampleSize '10' --regionSize '1'", "user_email": "tests@fake.org", "command_version": "computeGCBias 3.5.4", "params": {"source": "{\"__current_case__\": 1, \"input1\": {\"values\": [{\"id\": 14, \"src\": \"hda\"}]}, \"ref_source\": \"history\"}", "effectiveGenomeSize": "{\"__current_case__\": 0, \"effectiveGenomeSize\": \"10050\", \"effectiveGenomeSize_opt\": \"specific\"}", "fragmentLength": "\"300\"", "region": "\"chr2L\"", "advancedOpt": "{\"__current_case__\": 1, \"blackListFileName\": null, \"extraSampling\": null, \"regionSize\": \"1\", \"sampleSize\": \"10\", \"showAdvancedOpt\": \"yes\"}", "image_format": "\"none\"", "chromInfo": 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reference.kallisto --bootstrap-samples 0 --seed 42 --threads 8 -o . /galaxy/server/database/objects/e/9/5/dataset_e95b4223-5756-43f2-bce6-4ec286b0fcb9.dat /galaxy/server/database/objects/5/1/9/dataset_5190f3c3-b4f7-46f7-95f1-51bf2594faf3.dat\"\n}\n", "tool_stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/e/9/5/dataset_e95b4223-5756-43f2-bce6-4ec286b0fcb9.dat\n /galaxy/server/database/objects/5/1/9/dataset_5190f3c3-b4f7-46f7-95f1-51bf2594faf3.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 100 reads, 100 reads pseudoaligned\n[quant] estimated average fragment length: 499.12\n[ em] quantifying the abundances ... done\n[ em] the Expectation-Maximization algorithm ran for 52 rounds\n\n", "job_stdout": "", "job_stderr": "", "stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 100,\n\t\"n_pseudoaligned\": 100,\n\t\"n_unique\": 100,\n\t\"p_pseudoaligned\": 100.0,\n\t\"p_unique\": 100.0,\n\t\"kallisto_version\": \"0.48.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Nov 12 18:55:16 2024\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --threads 8 -o . /galaxy/server/database/objects/e/9/5/dataset_e95b4223-5756-43f2-bce6-4ec286b0fcb9.dat /galaxy/server/database/objects/5/1/9/dataset_5190f3c3-b4f7-46f7-95f1-51bf2594faf3.dat\"\n}\n", "stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/e/9/5/dataset_e95b4223-5756-43f2-bce6-4ec286b0fcb9.dat\n /galaxy/server/database/objects/5/1/9/dataset_5190f3c3-b4f7-46f7-95f1-51bf2594faf3.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 100 reads, 100 reads pseudoaligned\n[quant] estimated average fragment length: 499.12\n[ em] quantifying the abundances ... done\n[ em] the Expectation-Maximization algorithm ran for 52 rounds\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-12 18:55:16", "plugin": "core", "name": "end_epoch", "raw_value": "1731437716.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 18:55:16", "plugin": "core", "name": "start_epoch", "raw_value": "1731437716.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "kallisto_quant/0.48.0+galaxy1-1", "has_data": true, "data": {"tool_id": "kallisto_quant", "tool_version": "0.48.0+galaxy1", "test_index": 1, "time_seconds": 42.58518409729004, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "909b15a0a4975c7e"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|forward": {"src": "hda", "id": "cd8a2c7c5538f3b6"}, "single_paired|reverse": {"src": "hda", "id": "17e102e571ec9325"}, "single_paired|lib_type": "--fr-stranded", "single_paired|single_paired_selector": "paired_single"}, "job": {"model_class": "Job", "id": "e8b7d0422a3a8c75", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T18:55:58.086868", "update_time": "2024-11-12T18:56:12.254112", "galaxy_version": "24.1", "external_id": "gxy-kjcrx", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/6/0/1/dataset_60101091-e970-4f21-8b5c-a95ad95ae4d8.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto quant -i 'reference.kallisto' --bootstrap-samples 0 --seed 42 --threads ${GALAXY_SLOTS:-1} -o . --fr-stranded '/galaxy/server/database/objects/7/d/c/dataset_7dc8fcd9-a1cc-4a3f-ba17-7b14c95676c6.dat' '/galaxy/server/database/objects/c/5/b/dataset_c5b1aef6-0ae3-4fa2-a7d3-7e8fbe85f6dc.dat' && cat run_info.json", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"42\"", "genomebam_option": "{\"__current_case__\": 1, \"selector\": \"\"}", "pseudobam": "false", "single_overhang": "false", "fusion": "false", "bootstrap_samples": "\"0\"", "bias": "false", "single_paired": "{\"__current_case__\": 1, \"forward\": {\"values\": [{\"id\": 99, \"src\": \"hda\"}]}, \"lib_type\": \"--fr-stranded\", \"reverse\": {\"values\": [{\"id\": 100, \"src\": \"hda\"}]}, \"single_paired_selector\": \"paired_single\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 98, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "909b15a0a4975c7e", "src": "hda", "uuid": "60101091-e970-4f21-8b5c-a95ad95ae4d8"}, "single_paired|forward": {"id": "cd8a2c7c5538f3b6", "src": "hda", "uuid": "7dc8fcd9-a1cc-4a3f-ba17-7b14c95676c6"}, "single_paired|reverse": {"id": "17e102e571ec9325", "src": "hda", "uuid": "c5b1aef6-0ae3-4fa2-a7d3-7e8fbe85f6dc"}}, "outputs": {"abundance_h5": {"id": "2d3b334463434585", "src": "hda", "uuid": "59d8f200-8957-4751-bf70-70dc92422469"}, "abundance_tab": {"id": "a9ddc67bc0d83a6f", "src": "hda", "uuid": "0ddd72cb-2619-47d1-a206-d6a6060bcadc"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 100,\n\t\"n_pseudoaligned\": 37,\n\t\"n_unique\": 37,\n\t\"p_pseudoaligned\": 37.0,\n\t\"p_unique\": 37.0,\n\t\"kallisto_version\": \"0.48.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Nov 12 18:55:59 2024\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --threads 8 -o . --fr-stranded /galaxy/server/database/objects/7/d/c/dataset_7dc8fcd9-a1cc-4a3f-ba17-7b14c95676c6.dat /galaxy/server/database/objects/c/5/b/dataset_c5b1aef6-0ae3-4fa2-a7d3-7e8fbe85f6dc.dat\"\n}\n", "tool_stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/7/d/c/dataset_7dc8fcd9-a1cc-4a3f-ba17-7b14c95676c6.dat\n /galaxy/server/database/objects/c/5/b/dataset_c5b1aef6-0ae3-4fa2-a7d3-7e8fbe85f6dc.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 100 reads, 37 reads pseudoaligned\n[quant] estimated average fragment length: 495.838\n[ em] quantifying the abundances ... done\n[ em] the Expectation-Maximization algorithm ran for 52 rounds\n\n", "job_stdout": "", "job_stderr": "", "stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 100,\n\t\"n_pseudoaligned\": 37,\n\t\"n_unique\": 37,\n\t\"p_pseudoaligned\": 37.0,\n\t\"p_unique\": 37.0,\n\t\"kallisto_version\": \"0.48.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Nov 12 18:55:59 2024\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --threads 8 -o . --fr-stranded /galaxy/server/database/objects/7/d/c/dataset_7dc8fcd9-a1cc-4a3f-ba17-7b14c95676c6.dat /galaxy/server/database/objects/c/5/b/dataset_c5b1aef6-0ae3-4fa2-a7d3-7e8fbe85f6dc.dat\"\n}\n", "stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/7/d/c/dataset_7dc8fcd9-a1cc-4a3f-ba17-7b14c95676c6.dat\n /galaxy/server/database/objects/c/5/b/dataset_c5b1aef6-0ae3-4fa2-a7d3-7e8fbe85f6dc.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 100 reads, 37 reads pseudoaligned\n[quant] estimated average fragment length: 495.838\n[ em] quantifying the abundances ... done\n[ em] the Expectation-Maximization algorithm ran for 52 rounds\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-12 18:55:59", "plugin": "core", "name": "end_epoch", "raw_value": "1731437759.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 18:55:59", "plugin": "core", "name": "start_epoch", "raw_value": "1731437759.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "kallisto_quant/0.48.0+galaxy1-2", "has_data": true, "data": {"tool_id": "kallisto_quant", "tool_version": "0.48.0+galaxy1", "test_index": 2, "time_seconds": 12.581231117248535, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "kallisto_quant/0.48.0+galaxy1-3", "has_data": true, "data": {"tool_id": "kallisto_quant", "tool_version": "0.48.0+galaxy1", "test_index": 3, "time_seconds": 35.674410581588745, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "9fc274bfa9d71dff"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|reads": {"src": "hda", "id": "a042cd357bab67bc"}, "single_paired|single_paired_selector": "single"}, "job": {"model_class": "Job", "id": "58144eee3514d507", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T18:56:46.651616", "update_time": "2024-11-12T18:57:00.372226", "galaxy_version": "24.1", "external_id": "gxy-7rnpq", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/7/f/f/dataset_7ffcce7d-aead-42fc-b34f-9f109814bec7.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto quant -i 'reference.kallisto' --bootstrap-samples 0 --seed 42 --threads ${GALAXY_SLOTS:-1} -o . --single --fragment-length 200 --sd 20 '/galaxy/server/database/objects/e/6/1/dataset_e6153a41-1c19-46ae-990a-cf12e8039486.dat' && cat run_info.json", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"42\"", "genomebam_option": "{\"__current_case__\": 1, \"selector\": \"\"}", "pseudobam": "false", "single_overhang": "false", "fusion": "false", "bootstrap_samples": "\"0\"", "bias": "false", "single_paired": "{\"__current_case__\": 0, \"fragment_length\": \"200\", \"reads\": {\"values\": [{\"id\": 107, \"src\": \"hda\"}]}, \"sd\": \"20\", \"single_paired_selector\": \"single\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 106, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "9fc274bfa9d71dff", "src": "hda", "uuid": "7ffcce7d-aead-42fc-b34f-9f109814bec7"}, "single_paired|reads": {"id": "a042cd357bab67bc", "src": "hda", "uuid": "e6153a41-1c19-46ae-990a-cf12e8039486"}}, "outputs": {"abundance_h5": {"id": "86e62fa69f4abdb6", "src": "hda", "uuid": "a9ac5a4f-be1e-4614-9ea5-0f35bca2a57d"}, "abundance_tab": {"id": "ab93220ba3f66e53", "src": "hda", "uuid": "806a6c43-9b2f-475a-8f21-9352c1dee836"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 100,\n\t\"n_pseudoaligned\": 100,\n\t\"n_unique\": 100,\n\t\"p_pseudoaligned\": 100.0,\n\t\"p_unique\": 100.0,\n\t\"kallisto_version\": \"0.48.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Nov 12 18:56:48 2024\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --threads 8 -o . --single --fragment-length 200 --sd 20 /galaxy/server/database/objects/e/6/1/dataset_e6153a41-1c19-46ae-990a-cf12e8039486.dat\"\n}\n", "tool_stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in single-end mode\n[quant] will process file 1: /galaxy/server/database/objects/e/6/1/dataset_e6153a41-1c19-46ae-990a-cf12e8039486.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 100 reads, 100 reads pseudoaligned\n[ em] quantifying the abundances ... done\n[ em] the Expectation-Maximization algorithm ran for 52 rounds\n\n", "job_stdout": "", "job_stderr": "", "stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 100,\n\t\"n_pseudoaligned\": 100,\n\t\"n_unique\": 100,\n\t\"p_pseudoaligned\": 100.0,\n\t\"p_unique\": 100.0,\n\t\"kallisto_version\": \"0.48.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Nov 12 18:56:48 2024\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --threads 8 -o . --single --fragment-length 200 --sd 20 /galaxy/server/database/objects/e/6/1/dataset_e6153a41-1c19-46ae-990a-cf12e8039486.dat\"\n}\n", "stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1 contigs and contains 16269 k-mers \n\n\n[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,269\n[index] number of equivalence classes: 1\n[quant] running in single-end mode\n[quant] will process file 1: /galaxy/server/database/objects/e/6/1/dataset_e6153a41-1c19-46ae-990a-cf12e8039486.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 100 reads, 100 reads pseudoaligned\n[ em] quantifying the abundances ... done\n[ em] the Expectation-Maximization algorithm ran for 52 rounds\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-12 18:56:48", "plugin": "core", "name": "end_epoch", "raw_value": "1731437808.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 18:56:48", "plugin": "core", "name": "start_epoch", "raw_value": "1731437808.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "kallisto_quant/0.48.0+galaxy1-4", "has_data": true, "data": {"tool_id": "kallisto_quant", "tool_version": "0.48.0+galaxy1", "test_index": 4, "time_seconds": 42.279791593551636, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "31d5b366d40a8a7d"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|forward": {"src": "hda", "id": "e19a2a42d2c77e5c"}, "single_paired|reverse": {"src": "hda", "id": "361b9c563cfcdddf"}, "single_paired|single_paired_selector": "paired_single", "pseudobam": true}, "job": {"model_class": "Job", "id": "8c6a9b7b4f005250", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T18:57:28.519646", "update_time": "2024-11-12T18:57:42.347220", "galaxy_version": "24.1", "external_id": "gxy-t4c2d", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/4/1/b/dataset_41b3756a-8657-4b8b-8983-828720e2357b.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto quant -i 'reference.kallisto' --bootstrap-samples 0 --seed 42 --pseudobam -o . '/galaxy/server/database/objects/5/9/3/dataset_59387449-7e50-4b2a-8be9-e0a10fcdcb70.dat' '/galaxy/server/database/objects/a/5/c/dataset_a5c7378b-5ae7-48d0-9360-1e2121a07a65.dat' && samtools sort --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -T \"${TMPDIR:-.}\" -o '/galaxy/server/database/objects/a/8/e/dataset_a8ea8f1e-f283-406b-945c-82a14c482171.dat' pseudoalignments.bam && cat run_info.json", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"42\"", "genomebam_option": "{\"__current_case__\": 1, \"selector\": \"\"}", "pseudobam": "true", "single_overhang": "false", "fusion": "false", "bootstrap_samples": "\"0\"", "bias": "false", "single_paired": "{\"__current_case__\": 1, \"forward\": {\"values\": [{\"id\": 111, \"src\": \"hda\"}]}, \"lib_type\": \"\", \"reverse\": {\"values\": [{\"id\": 112, \"src\": \"hda\"}]}, \"single_paired_selector\": \"paired_single\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 110, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "31d5b366d40a8a7d", "src": "hda", "uuid": "41b3756a-8657-4b8b-8983-828720e2357b"}, "single_paired|forward": {"id": "e19a2a42d2c77e5c", "src": "hda", "uuid": "59387449-7e50-4b2a-8be9-e0a10fcdcb70"}, "single_paired|reverse": {"id": "361b9c563cfcdddf", "src": "hda", "uuid": "a5c7378b-5ae7-48d0-9360-1e2121a07a65"}}, "outputs": {"abundance_h5": {"id": "9942918c56ad7f5a", "src": "hda", "uuid": "be853bf7-d5bd-4f5f-91dc-3c7c473255b1"}, "abundance_tab": {"id": "5784b744b12f0660", "src": "hda", "uuid": "54f6068c-cc42-4dda-bceb-9b1f6751e6ed"}, "pseudobam_output": {"id": "f01e3d765cb45d79", "src": "hda", "uuid": "a8ea8f1e-f283-406b-945c-82a14c482171"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 200,\n\t\"n_pseudoaligned\": 200,\n\t\"n_unique\": 200,\n\t\"p_pseudoaligned\": 100.0,\n\t\"p_unique\": 100.0,\n\t\"kallisto_version\": \"0.48.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Nov 12 18:57:30 2024\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --pseudobam -o . /galaxy/server/database/objects/5/9/3/dataset_59387449-7e50-4b2a-8be9-e0a10fcdcb70.dat /galaxy/server/database/objects/a/5/c/dataset_a5c7378b-5ae7-48d0-9360-1e2121a07a65.dat\"\n}\n", "tool_stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 15 contigs and contains 16670 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,670\n[index] number of equivalence classes: 1\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/5/9/3/dataset_59387449-7e50-4b2a-8be9-e0a10fcdcb70.dat\n /galaxy/server/database/objects/a/5/c/dataset_a5c7378b-5ae7-48d0-9360-1e2121a07a65.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 200 reads, 200 reads pseudoaligned\n[quant] estimated average fragment length: 500.01\n[ em] quantifying the abundances ... done\n[ em] the Expectation-Maximization algorithm ran for 52 rounds\n[ bam] writing pseudoalignments to BAM format .. done\n\n", "job_stdout": "", "job_stderr": "", "stdout": "{\n\t\"n_targets\": 1,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 200,\n\t\"n_pseudoaligned\": 200,\n\t\"n_unique\": 200,\n\t\"p_pseudoaligned\": 100.0,\n\t\"p_unique\": 100.0,\n\t\"kallisto_version\": \"0.48.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Nov 12 18:57:30 2024\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --pseudobam -o . /galaxy/server/database/objects/5/9/3/dataset_59387449-7e50-4b2a-8be9-e0a10fcdcb70.dat /galaxy/server/database/objects/a/5/c/dataset_a5c7378b-5ae7-48d0-9360-1e2121a07a65.dat\"\n}\n", "stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 15 contigs and contains 16670 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 1\n[index] number of k-mers: 16,670\n[index] number of equivalence classes: 1\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/5/9/3/dataset_59387449-7e50-4b2a-8be9-e0a10fcdcb70.dat\n /galaxy/server/database/objects/a/5/c/dataset_a5c7378b-5ae7-48d0-9360-1e2121a07a65.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 200 reads, 200 reads pseudoaligned\n[quant] estimated average fragment length: 500.01\n[ em] quantifying the abundances ... done\n[ em] the Expectation-Maximization algorithm ran for 52 rounds\n[ bam] writing pseudoalignments to BAM format .. done\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-12 18:57:30", "plugin": "core", "name": "end_epoch", "raw_value": "1731437850.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 18:57:30", "plugin": "core", "name": "start_epoch", "raw_value": "1731437850.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "kallisto_quant/0.48.0+galaxy1-5", "has_data": true, "data": {"tool_id": "kallisto_quant", "tool_version": "0.48.0+galaxy1", "test_index": 5, "time_seconds": 21.87810230255127, "inputs": {"single_paired|forward": {"src": "hda", "id": "680541cf772f940a"}, "single_paired|reverse": {"src": "hda", "id": "bd5d21d926d0e24f"}, "single_paired|single_paired_selector": "paired_single", "pseudobam": true}, "execution_problem": "parameter 'index': an invalid option (None) was selected, please verify", "dynamic_param_error": true, "status": "error"}}, {"id": "kallisto_quant/0.48.0+galaxy1-6", "has_data": true, "data": {"tool_id": "kallisto_quant", "tool_version": "0.48.0+galaxy1", "test_index": 6, "time_seconds": 43.00889468193054, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "43dd47fc03a922dc"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|forward": {"src": "hda", "id": "131fdfbf0346cb1a"}, "single_paired|reverse": {"src": "hda", "id": "565c15e90e40f485"}, "single_paired|single_paired_selector": "paired_single", "fusion": true}, "job": {"model_class": "Job", "id": "6e1c2e6968a87ac8", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T18:58:32.251288", "update_time": "2024-11-12T18:58:47.746222", "galaxy_version": "24.1", "external_id": "gxy-v9h67", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/a/4/2/dataset_a42417ad-3552-4e93-8ebb-dbc91ee84487.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto quant -i 'reference.kallisto' --bootstrap-samples 0 --seed 42 --fusion --threads ${GALAXY_SLOTS:-1} -o . '/galaxy/server/database/objects/5/e/7/dataset_5e745d63-718a-4776-96c0-59168fd63623.dat' '/galaxy/server/database/objects/1/2/3/dataset_12346b85-2bd3-46c9-acc3-ddc402210b36.dat' && cat run_info.json", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"hg38\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg38.len\"", "seed": "\"42\"", "genomebam_option": "{\"__current_case__\": 1, \"selector\": \"\"}", "pseudobam": "false", "single_overhang": "false", "fusion": "true", "bootstrap_samples": "\"0\"", "bias": "false", "single_paired": "{\"__current_case__\": 1, \"forward\": {\"values\": [{\"id\": 119, \"src\": \"hda\"}]}, \"lib_type\": \"\", \"reverse\": {\"values\": [{\"id\": 120, \"src\": \"hda\"}]}, \"single_paired_selector\": \"paired_single\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 118, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "43dd47fc03a922dc", "src": "hda", "uuid": "a42417ad-3552-4e93-8ebb-dbc91ee84487"}, "single_paired|forward": {"id": "131fdfbf0346cb1a", "src": "hda", "uuid": "5e745d63-718a-4776-96c0-59168fd63623"}, "single_paired|reverse": {"id": "565c15e90e40f485", "src": "hda", "uuid": "12346b85-2bd3-46c9-acc3-ddc402210b36"}}, "outputs": {"abundance_h5": {"id": "aa1970df5d90212f", "src": "hda", "uuid": "8d54268e-d9eb-446f-8624-d4931c8948d4"}, "abundance_tab": {"id": "50a349429066c0ac", "src": "hda", "uuid": "e96535d5-13de-4f0b-bb5e-010814c518a3"}, "fusion_output": {"id": "86e354b1a2664edb", "src": "hda", "uuid": "b92caecf-7989-4ca4-ae43-d9f3c3ce253b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "{\n\t\"n_targets\": 284,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 744,\n\t\"n_pseudoaligned\": 368,\n\t\"n_unique\": 263,\n\t\"p_pseudoaligned\": 49.5,\n\t\"p_unique\": 35.3,\n\t\"kallisto_version\": \"0.48.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Nov 12 18:58:34 2024\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --fusion --threads 8 -o . /galaxy/server/database/objects/5/e/7/dataset_5e745d63-718a-4776-96c0-59168fd63623.dat /galaxy/server/database/objects/1/2/3/dataset_12346b85-2bd3-46c9-acc3-ddc402210b36.dat\"\n}\n", "tool_stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] warning: clipped off poly-A tail (longer than 10)\n from 7 target sequences\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1179 contigs and contains 216490 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 284\n[index] number of k-mers: 216,490\n[index] number of equivalence classes: 909\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/5/e/7/dataset_5e745d63-718a-4776-96c0-59168fd63623.dat\n /galaxy/server/database/objects/1/2/3/dataset_12346b85-2bd3-46c9-acc3-ddc402210b36.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 744 reads, 368 reads pseudoaligned\n[quant] estimated average fragment length: 140.96\n[ em] quantifying the abundances ... done\n[ em] the Expectation-Maximization algorithm ran for 210 rounds\n\n", "job_stdout": "", "job_stderr": "", "stdout": "{\n\t\"n_targets\": 284,\n\t\"n_bootstraps\": 0,\n\t\"n_processed\": 744,\n\t\"n_pseudoaligned\": 368,\n\t\"n_unique\": 263,\n\t\"p_pseudoaligned\": 49.5,\n\t\"p_unique\": 35.3,\n\t\"kallisto_version\": \"0.48.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Nov 12 18:58:34 2024\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --fusion --threads 8 -o . /galaxy/server/database/objects/5/e/7/dataset_5e745d63-718a-4776-96c0-59168fd63623.dat /galaxy/server/database/objects/1/2/3/dataset_12346b85-2bd3-46c9-acc3-ddc402210b36.dat\"\n}\n", "stderr": "\n[build] loading fasta file reference.fa\n[build] k-mer length: 31\n[build] warning: clipped off poly-A tail (longer than 10)\n from 7 target sequences\n[build] counting k-mers ... done.\n[build] building target de Bruijn graph ... done \n[build] creating equivalence classes ... done\n[build] target de Bruijn graph has 1179 contigs and contains 216490 k-mers \n\n\n[quant] fragment length distribution will be estimated from the data\n[index] k-mer length: 31\n[index] number of targets: 284\n[index] number of k-mers: 216,490\n[index] number of equivalence classes: 909\n[quant] running in paired-end mode\n[quant] will process pair 1: /galaxy/server/database/objects/5/e/7/dataset_5e745d63-718a-4776-96c0-59168fd63623.dat\n /galaxy/server/database/objects/1/2/3/dataset_12346b85-2bd3-46c9-acc3-ddc402210b36.dat\n[quant] finding pseudoalignments for the reads ... done\n[quant] processed 744 reads, 368 reads pseudoaligned\n[quant] estimated average fragment length: 140.96\n[ em] quantifying the abundances ... done\n[ em] the Expectation-Maximization algorithm ran for 210 rounds\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-11-12 18:58:34", "plugin": "core", "name": "end_epoch", "raw_value": "1731437914.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 18:58:34", "plugin": "core", "name": "start_epoch", "raw_value": "1731437914.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "kallisto_quant/0.48.0+galaxy1-7", "has_data": true, "data": {"tool_id": "kallisto_quant", "tool_version": "0.48.0+galaxy1", "test_index": 7, "time_seconds": 12.480783462524414, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "mummer_show_coords/4.0.0rc1+galaxy3-0", "has_data": true, "data": {"tool_id": "mummer_show_coords", "tool_version": "4.0.0rc1+galaxy3", "test_index": 0, "time_seconds": 33.628251791000366, "inputs": {"delta": {"src": "hda", "id": "58144eee3514d507"}}, "job": {"model_class": "Job", "id": "eee892f340a734c7", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3", "state": "error", "exit_code": null, "create_time": "2024-11-12T18:52:22.806498", "update_time": "2024-11-12T18:52:35.029337", "galaxy_version": "24.1", "external_id": "gxy-lp8s7", "handler": null, "job_runner_name": null, "command_line": "show-coords -c -H -I '75.0' -l -L '100' -q -T '/galaxy/server/database/objects/8/8/5/dataset_885655b8-d1ab-4de1-8560-ec71a595f2a1.dat' > '/galaxy/server/database/objects/3/7/3/dataset_3737b0b6-e3f6-441d-9062-28a61e89dfb8.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sort": "\"-q\"", "annotate": "false", "min_alignment_length": "\"100\"", "identity": "\"75.0\"", "merge": "false"}, "inputs": {"delta": {"id": "58144eee3514d507", "src": "hda", "uuid": "885655b8-d1ab-4de1-8560-ec71a595f2a1"}}, "outputs": {"output": {"id": "2d95868d81555422", "src": "hda", "uuid": "3737b0b6-e3f6-441d-9062-28a61e89dfb8"}}, "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/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0rc1+galaxy3, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "music_inspect_eset/0.1.1+galaxy0-0", "has_data": true, "data": {"tool_id": "music_inspect_eset", "tool_version": "0.1.1+galaxy0", "test_index": 0, "time_seconds": 13.58507752418518, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "music_inspect_eset/0.1.1+galaxy0-0", "has_data": true, "data": {"tool_id": "music_inspect_eset", "tool_version": "0.1.1+galaxy0", "test_index": 0, "time_seconds": 41.485530376434326, "inputs": {"rds_eset": {"src": "hda", "id": "d7a8c3e6bbd352d3"}, "inspector": "print"}, "job": {"model_class": "Job", "id": "43dd47fc03a922dc", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:06:56.901984", "update_time": "2024-11-12T19:07:15.686466", "galaxy_version": "24.1", "external_id": "gxy-tqk2z", "handler": null, "job_runner_name": null, "command_line": "Rscript --vanilla '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/2fed32b5aa02/music_inspect_eset/scripts/inspect.R' '/galaxy/server/database/jobs_directory/000/118/configs/tmpnt8q3gev'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "inspector": "\"print\""}, "inputs": {"rds_eset": {"id": "d7a8c3e6bbd352d3", "src": "hda", "uuid": "5a956a1b-1708-4c4a-adde-fcdf5d2da527"}}, "outputs": {"out_tab": {"id": "f7b695b1a284d214", "src": "hda", "uuid": "c9371159-aa1b-446e-a4be-7d3d0ed2f2a1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "ExpressionSet (storageMode: lockedEnvironment)\nassayData: 2066 features, 250 samples \n element names: exprs \nprotocolData: none\nphenoData\n sampleNames: AZ_A10 AZ_A11 ... HP1502401_K15 (250 total)\n varLabels: sampleID SubjectName cellTypeID cellType\n varMetadata: labelDescription\nfeatureData: none\nexperimentData: use 'experimentData(object)'\nAnnotation: \n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "ExpressionSet (storageMode: lockedEnvironment)\nassayData: 2066 features, 250 samples \n element names: exprs \nprotocolData: none\nphenoData\n sampleNames: AZ_A10 AZ_A11 ... HP1502401_K15 (250 total)\n varLabels: sampleID SubjectName cellTypeID cellType\n varMetadata: labelDescription\nfeatureData: none\nexperimentData: use 'experimentData(object)'\nAnnotation: \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": "2024-11-12 19:07:03", "plugin": "core", "name": "end_epoch", "raw_value": "1731438423.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:06:58", "plugin": "core", "name": "start_epoch", "raw_value": "1731438418.0000000"}, {"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": "music_inspect_eset/0.1.1+galaxy0-1", "has_data": true, 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Aborting.\" 1>&2; exit 1; } } && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'gff3' ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ignore_failed": "\"0\"", "range": null, "molecule": "{\"__current_case__\": 0, \"format\": \"gff3\", \"select\": \"nucleotide\"}", "query_source": "{\"__current_case__\": 0, \"accession_file\": {\"values\": [{\"id\": 53, \"src\": \"hda\"}]}, \"select\": \"accession_file\"}"}, "inputs": {"query_source|accession_file": {"id": "e31e59d6c2852311", "src": "hda", "uuid": "0ac4908a-598e-4828-a366-e9c64b950d86"}}, "outputs": {"error_log": {"id": "842b6a351587ff3b", "src": "hda", "uuid": "91fde7b4-0b0e-427a-8bd7-950664e8f2c0"}, "__new_primary_file_output|CP011064__": {"id": "a0e3c015f452297d", "src": "hda", "uuid": "205ec115-7777-4e6d-80d7-6259e0010579"}, "__new_primary_file_output|CP021680__": {"id": "029e02c70d71eef6", "src": "hda", "uuid": "7b9208d9-0237-462f-a963-296723d73494"}}, "copied_from_job_id": null, "output_collections": {"output": {"src": "hdca", "id": "01b458aaa384e315"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "8 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "8.0000000"}, {"title": "Job End Time", "value": "2024-11-12 18:48:50", "plugin": "core", "name": "end_epoch", "raw_value": "1731437330.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 18:48:42", "plugin": "core", "name": "start_epoch", "raw_value": "1731437322.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "ncbi_acc_download/0.2.8+galaxy0-3", "has_data": true, "data": {"tool_id": "ncbi_acc_download", "tool_version": "0.2.8+galaxy0", "test_index": 3, "time_seconds": 42.54658579826355, "inputs": {"query_source|accession_file": {"src": "hda", "id": "6eb7d1a976e3e08a"}, "query_source|select": "accession_file", "molecule|format": "featuretable", "molecule|select": "nucleotide"}, "job": {"model_class": "Job", "id": "b1dab936a2e42164", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T18:49:25.185916", "update_time": "2024-11-12T18:49:45.254482", "galaxy_version": "24.1", "external_id": "gxy-vlnrx", "handler": null, "job_runner_name": null, "command_line": "{ grep -v \"^[ \\t]*$\" /galaxy/server/database/objects/6/a/e/dataset_6aeb89cd-c9d9-489c-829d-5efb6e941747.dat > accessions || { echo \"No accession numbers in input. 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\"no\"}", "plotsym": "{\"__current_case__\": 0, \"do_opt\": \"no\"}", "plotgen": "{\"__current_case__\": 1, \"clusts_plot\": \"\", \"do_opt\": \"yes\"}"}, "inputs": {"inputrds": {"id": "fd4a77e3c68c4733", "src": "hda", "uuid": "1f854d22-c98e-4793-bef6-a61273cb01c8"}}, "outputs": {"outpdf": {"id": "e5526711daf3c91e", "src": "hda", "uuid": "660a0f32-7773-45ba-8fb9-1243484dabf6"}, "outlog": {"id": "e66eb01a20ac288d", "src": "hda", "uuid": "38662a0b-b9ad-4636-b074-38c6e78ccc48"}}, "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": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-11-12 19:15:49", "plugin": "core", "name": "end_epoch", "raw_value": "1731438949.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:15:45", "plugin": "core", "name": "start_epoch", "raw_value": "1731438945.0000000"}, {"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": "racon/1.5.0+galaxy1-0", "has_data": true, "data": {"tool_id": "racon", "tool_version": "1.5.0+galaxy1", "test_index": 0, "time_seconds": 82.31148266792297, "inputs": {"reads": {"src": "hda", "id": "aff48f2f86cebb71"}, "overlaps": {"src": "hda", "id": "21769672057c80ef"}, "corrected_reads": {"src": "hda", "id": "01b458aaa384e315"}, "include_unpolished": true, "fragment_correction": true, "window_length": "800", "error_threshold": "0.2"}, "job": {"model_class": "Job", "id": "289239a5aa6459ef", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T18:34:51.924880", "update_time": "2024-11-12T18:35:41.695104", "galaxy_version": "24.1", "external_id": "gxy-nx27w", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/a/f/c/dataset_afc1ba3e-8677-4116-9083-0e959a2f2fdb.dat' reads.fasta && ln -s '/galaxy/server/database/objects/2/2/f/dataset_22fa02ec-c275-4775-8068-e378452285c0.dat' overlaps.sam && ln -s '/galaxy/server/database/objects/5/5/e/dataset_55ec6a70-4424-4287-b3f9-d16cac80a8fc.dat' corrected_reads.fasta && racon reads.fasta overlaps.sam corrected_reads.fasta -t ${GALAXY_SLOTS:-4} -u -f -w 800 -q 10.0 -e 0.2 -m 3 -x -5 -g -4 > racon_polished_consensus.fa", "user_email": "tests@fake.org", "command_version": "1.5.0", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "gap": "\"-4\"", "mismatch": "\"-5\"", "match": "\"3\"", "no_trimming": "false", "error_threshold": "\"0.2\"", "quality_threshold": "\"10.0\"", "window_length": "\"800\"", "fragment_correction": "true", "include_unpolished": "true"}, "inputs": {"corrected_reads": {"id": "01b458aaa384e315", "src": "hda", "uuid": "55ec6a70-4424-4287-b3f9-d16cac80a8fc"}, "overlaps": {"id": "21769672057c80ef", "src": "hda", "uuid": "22fa02ec-c275-4775-8068-e378452285c0"}, "reads": {"id": "aff48f2f86cebb71", "src": "hda", "uuid": "afc1ba3e-8677-4116-9083-0e959a2f2fdb"}}, "outputs": {"consensus": {"id": "289239a5aa6459ef", "src": "hda", "uuid": "11e670f6-245c-40de-967b-fe49b03a731a"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[racon::Polisher::initialize] loaded target sequences 0.001004 s\n[racon::Polisher::initialize] loaded sequences 0.010254 s\n[racon::Polisher::initialize] loaded overlaps 0.011991 s\n[racon::Polisher::initialize] aligning overlaps [=> ] 0.002004 s\r[racon::Polisher::initialize] aligning overlaps [==> ] 0.002074 s\r[racon::Polisher::initialize] aligning overlaps [===> ] 0.002159 s\r[racon::Polisher::initialize] aligning overlaps [====> ] 0.002234 s\r[racon::Polisher::initialize] aligning overlaps [=====> ] 0.002394 s\r[racon::Polisher::initialize] aligning overlaps [======> ] 0.002478 s\r[racon::Polisher::initialize] aligning overlaps [=======> ] 0.002574 s\r[racon::Polisher::initialize] aligning overlaps [========> ] 0.002673 s\r[racon::Polisher::initialize] aligning overlaps [=========> ] 0.002785 s\r[racon::Polisher::initialize] aligning overlaps [==========> ] 0.002868 s\r[racon::Polisher::initialize] aligning overlaps [===========> ] 0.002986 s\r[racon::Polisher::initialize] aligning overlaps [============> ] 0.003123 s\r[racon::Polisher::initialize] aligning overlaps [=============> ] 0.003245 s\r[racon::Polisher::initialize] aligning overlaps [==============> ] 0.003260 s\r[racon::Polisher::initialize] aligning overlaps [===============> ] 0.003316 s\r[racon::Polisher::initialize] aligning overlaps [================> ] 0.003439 s\r[racon::Polisher::initialize] aligning overlaps [=================> ] 0.003455 s\r[racon::Polisher::initialize] aligning overlaps [==================> ] 0.003468 s\r[racon::Polisher::initialize] aligning overlaps [===================>] 0.003582 s\r[racon::Polisher::initialize] aligning overlaps [====================] 0.003596 s\n[racon::Polisher::initialize] transformed data into windows 0.000244 s\n[racon::Polisher::polish] generating consensus [=> ] 0.053768 s\r[racon::Polisher::polish] generating consensus [==> ] 0.054242 s\r[racon::Polisher::polish] generating consensus [===> ] 0.086715 s\r[racon::Polisher::polish] generating consensus [====> ] 0.086876 s\r[racon::Polisher::polish] generating consensus [=====> ] 0.086894 s\r[racon::Polisher::polish] generating consensus [======> ] 0.107319 s\r[racon::Polisher::polish] generating consensus [=======> ] 0.107352 s\r[racon::Polisher::polish] generating consensus [========> ] 0.110473 s\r[racon::Polisher::polish] generating consensus [=========> ] 0.162344 s\r[racon::Polisher::polish] generating consensus [==========> ] 0.169724 s\r[racon::Polisher::polish] generating consensus [===========> ] 0.253804 s\r[racon::Polisher::polish] generating consensus [============> ] 0.256505 s\r[racon::Polisher::polish] generating consensus [=============> ] 0.256539 s\r[racon::Polisher::polish] generating consensus [==============> ] 0.327457 s\r[racon::Polisher::polish] generating consensus [===============> ] 0.327752 s\r[racon::Polisher::polish] generating consensus [================> ] 0.334033 s\r[racon::Polisher::polish] generating consensus [=================> ] 0.345194 s\r[racon::Polisher::polish] generating consensus [==================> ] 0.358550 s\r[racon::Polisher::polish] generating consensus [===================>] 0.413721 s\r[racon::Polisher::polish] generating consensus [====================] 0.413789 s\n[racon::Polisher::] total = 0.444241 s\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[racon::Polisher::initialize] loaded target sequences 0.001004 s\n[racon::Polisher::initialize] loaded sequences 0.010254 s\n[racon::Polisher::initialize] loaded overlaps 0.011991 s\n[racon::Polisher::initialize] aligning overlaps [=> ] 0.002004 s\r[racon::Polisher::initialize] aligning overlaps [==> ] 0.002074 s\r[racon::Polisher::initialize] aligning overlaps [===> ] 0.002159 s\r[racon::Polisher::initialize] aligning overlaps [====> ] 0.002234 s\r[racon::Polisher::initialize] aligning overlaps [=====> ] 0.002394 s\r[racon::Polisher::initialize] aligning overlaps [======> ] 0.002478 s\r[racon::Polisher::initialize] aligning overlaps [=======> ] 0.002574 s\r[racon::Polisher::initialize] aligning overlaps [========> ] 0.002673 s\r[racon::Polisher::initialize] aligning overlaps [=========> ] 0.002785 s\r[racon::Polisher::initialize] aligning overlaps [==========> ] 0.002868 s\r[racon::Polisher::initialize] aligning overlaps [===========> ] 0.002986 s\r[racon::Polisher::initialize] aligning overlaps [============> ] 0.003123 s\r[racon::Polisher::initialize] aligning overlaps [=============> ] 0.003245 s\r[racon::Polisher::initialize] aligning overlaps [==============> ] 0.003260 s\r[racon::Polisher::initialize] aligning overlaps [===============> ] 0.003316 s\r[racon::Polisher::initialize] aligning overlaps [================> ] 0.003439 s\r[racon::Polisher::initialize] aligning overlaps [=================> ] 0.003455 s\r[racon::Polisher::initialize] aligning overlaps [==================> ] 0.003468 s\r[racon::Polisher::initialize] aligning overlaps [===================>] 0.003582 s\r[racon::Polisher::initialize] aligning overlaps [====================] 0.003596 s\n[racon::Polisher::initialize] transformed data into windows 0.000244 s\n[racon::Polisher::polish] generating consensus [=> ] 0.053768 s\r[racon::Polisher::polish] generating consensus [==> ] 0.054242 s\r[racon::Polisher::polish] generating consensus [===> ] 0.086715 s\r[racon::Polisher::polish] generating consensus [====> ] 0.086876 s\r[racon::Polisher::polish] generating consensus [=====> ] 0.086894 s\r[racon::Polisher::polish] generating consensus [======> ] 0.107319 s\r[racon::Polisher::polish] generating consensus [=======> ] 0.107352 s\r[racon::Polisher::polish] generating consensus [========> ] 0.110473 s\r[racon::Polisher::polish] generating consensus [=========> ] 0.162344 s\r[racon::Polisher::polish] generating consensus [==========> ] 0.169724 s\r[racon::Polisher::polish] generating consensus [===========> ] 0.253804 s\r[racon::Polisher::polish] generating consensus [============> ] 0.256505 s\r[racon::Polisher::polish] generating consensus [=============> ] 0.256539 s\r[racon::Polisher::polish] generating consensus [==============> ] 0.327457 s\r[racon::Polisher::polish] generating consensus [===============> ] 0.327752 s\r[racon::Polisher::polish] generating consensus [================> ] 0.334033 s\r[racon::Polisher::polish] generating consensus [=================> ] 0.345194 s\r[racon::Polisher::polish] generating consensus [==================> ] 0.358550 s\r[racon::Polisher::polish] generating consensus [===================>] 0.413721 s\r[racon::Polisher::polish] generating consensus [====================] 0.413789 s\n[racon::Polisher::] total = 0.444241 s\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": "2024-11-12 18:35:28", "plugin": "core", "name": "end_epoch", "raw_value": "1731436528.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 18:35:27", "plugin": "core", "name": "start_epoch", "raw_value": "1731436527.0000000"}, {"title": "Memory Allocated (MB)", "value": "38654", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "38654.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "racon/1.5.0+galaxy1-1", "has_data": true, "data": {"tool_id": "racon", "tool_version": "1.5.0+galaxy1", "test_index": 1, "time_seconds": 42.650673389434814, "inputs": {"reads": {"src": "hda", "id": "0d886783c55b40ad"}, "overlaps": {"src": "hda", "id": "6e73a15cbaf5030b"}, "corrected_reads": {"src": "hda", "id": "494cbb69761ccd75"}}, "job": {"model_class": "Job", "id": "919ed9e80b102f05", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T18:36:10.193813", "update_time": "2024-11-12T18:36:24.475282", "galaxy_version": "24.1", "external_id": "gxy-h9kw9", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/c/8/7/dataset_c87407ff-79ac-42e3-9cf2-3205982fb83e.dat' reads.fasta && ln -s '/galaxy/server/database/objects/6/c/6/dataset_6c62f16a-e59a-4ac2-af57-9bcf463c7d84.dat' overlaps.paf && ln -s '/galaxy/server/database/objects/a/4/d/dataset_a4dc9b73-02ee-4396-afe1-7c48db66179a.dat' corrected_reads.fasta && racon reads.fasta overlaps.paf corrected_reads.fasta -t ${GALAXY_SLOTS:-4} -w 500 -q 10.0 -e 0.3 -m 3 -x -5 -g -4 > racon_polished_consensus.fa", "user_email": "tests@fake.org", "command_version": "1.5.0", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "gap": "\"-4\"", "mismatch": "\"-5\"", "match": "\"3\"", "no_trimming": "false", "error_threshold": "\"0.3\"", "quality_threshold": "\"10.0\"", "window_length": "\"500\"", "fragment_correction": "false", "include_unpolished": "false"}, "inputs": {"corrected_reads": {"id": "494cbb69761ccd75", "src": "hda", "uuid": "a4dc9b73-02ee-4396-afe1-7c48db66179a"}, "overlaps": {"id": "6e73a15cbaf5030b", "src": "hda", "uuid": "6c62f16a-e59a-4ac2-af57-9bcf463c7d84"}, "reads": {"id": "0d886783c55b40ad", "src": "hda", "uuid": "c87407ff-79ac-42e3-9cf2-3205982fb83e"}}, "outputs": {"consensus": {"id": "919ed9e80b102f05", "src": "hda", "uuid": "6bb8466d-1f7e-419c-a159-85fbde089373"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[racon::Polisher::initialize] loaded target sequences 0.000847 s\n[racon::Polisher::initialize] loaded sequences 0.010134 s\n[racon::Polisher::initialize] loaded overlaps 0.000487 s\n[racon::Polisher::initialize] aligning overlaps [=> ] 0.013436 s\r[racon::Polisher::initialize] aligning overlaps [==> ] 0.019887 s\r[racon::Polisher::initialize] aligning overlaps [===> ] 0.027513 s\r[racon::Polisher::initialize] aligning overlaps [====> ] 0.030065 s\r[racon::Polisher::initialize] aligning overlaps [=====> ] 0.035204 s\r[racon::Polisher::initialize] aligning overlaps [======> ] 0.035404 s\r[racon::Polisher::initialize] aligning overlaps [=======> ] 0.043280 s\r[racon::Polisher::initialize] aligning overlaps [========> ] 0.049571 s\r[racon::Polisher::initialize] aligning overlaps [=========> ] 0.052633 s\r[racon::Polisher::initialize] aligning overlaps [==========> ] 0.056856 s\r[racon::Polisher::initialize] aligning overlaps [===========> ] 0.059797 s\r[racon::Polisher::initialize] aligning overlaps [============> ] 0.064315 s\r[racon::Polisher::initialize] aligning overlaps [=============> ] 0.074479 s\r[racon::Polisher::initialize] aligning overlaps [==============> ] 0.077366 s\r[racon::Polisher::initialize] aligning overlaps [===============> ] 0.091554 s\r[racon::Polisher::initialize] aligning overlaps [================> ] 0.101872 s\r[racon::Polisher::initialize] aligning overlaps [=================> ] 0.109477 s\r[racon::Polisher::initialize] aligning overlaps [==================> ] 0.110131 s\r[racon::Polisher::initialize] aligning overlaps [===================>] 0.110152 s\r[racon::Polisher::initialize] aligning overlaps [====================] 0.113696 s\n[racon::Polisher::initialize] transformed data into windows 0.000346 s\n[racon::Polisher::polish] generating consensus [=> ] 0.020773 s\r[racon::Polisher::polish] generating consensus [==> ] 0.021827 s\r[racon::Polisher::polish] generating consensus [===> ] 0.040910 s\r[racon::Polisher::polish] generating consensus [====> ] 0.041045 s\r[racon::Polisher::polish] generating consensus [=====> ] 0.051303 s\r[racon::Polisher::polish] generating consensus [======> ] 0.051497 s\r[racon::Polisher::polish] generating consensus [=======> ] 0.058868 s\r[racon::Polisher::polish] generating consensus [========> ] 0.058934 s\r[racon::Polisher::polish] generating consensus [=========> ] 0.068434 s\r[racon::Polisher::polish] generating consensus [==========> ] 0.068462 s\r[racon::Polisher::polish] generating consensus [===========> ] 0.086587 s\r[racon::Polisher::polish] generating consensus [============> ] 0.086614 s\r[racon::Polisher::polish] generating consensus [=============> ] 0.118306 s\r[racon::Polisher::polish] generating consensus [==============> ] 0.120215 s\r[racon::Polisher::polish] generating consensus [===============> ] 0.148133 s\r[racon::Polisher::polish] generating consensus [================> ] 0.160936 s\r[racon::Polisher::polish] generating consensus [=================> ] 0.173231 s\r[racon::Polisher::polish] generating consensus [==================> ] 0.173879 s\r[racon::Polisher::polish] generating consensus [===================>] 0.189225 s\r[racon::Polisher::polish] generating consensus [====================] 0.237113 s\n[racon::Polisher::] total = 0.365879 s\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[racon::Polisher::initialize] loaded target sequences 0.000847 s\n[racon::Polisher::initialize] loaded sequences 0.010134 s\n[racon::Polisher::initialize] loaded overlaps 0.000487 s\n[racon::Polisher::initialize] aligning overlaps [=> ] 0.013436 s\r[racon::Polisher::initialize] aligning overlaps [==> ] 0.019887 s\r[racon::Polisher::initialize] aligning overlaps [===> ] 0.027513 s\r[racon::Polisher::initialize] aligning overlaps [====> ] 0.030065 s\r[racon::Polisher::initialize] aligning overlaps [=====> ] 0.035204 s\r[racon::Polisher::initialize] aligning overlaps [======> ] 0.035404 s\r[racon::Polisher::initialize] aligning overlaps [=======> ] 0.043280 s\r[racon::Polisher::initialize] aligning overlaps [========> ] 0.049571 s\r[racon::Polisher::initialize] aligning overlaps [=========> ] 0.052633 s\r[racon::Polisher::initialize] aligning overlaps [==========> ] 0.056856 s\r[racon::Polisher::initialize] aligning overlaps [===========> ] 0.059797 s\r[racon::Polisher::initialize] aligning overlaps [============> ] 0.064315 s\r[racon::Polisher::initialize] aligning overlaps [=============> ] 0.074479 s\r[racon::Polisher::initialize] aligning overlaps [==============> ] 0.077366 s\r[racon::Polisher::initialize] aligning overlaps [===============> ] 0.091554 s\r[racon::Polisher::initialize] aligning overlaps [================> ] 0.101872 s\r[racon::Polisher::initialize] aligning overlaps [=================> ] 0.109477 s\r[racon::Polisher::initialize] aligning overlaps [==================> ] 0.110131 s\r[racon::Polisher::initialize] aligning overlaps [===================>] 0.110152 s\r[racon::Polisher::initialize] aligning overlaps [====================] 0.113696 s\n[racon::Polisher::initialize] transformed data into windows 0.000346 s\n[racon::Polisher::polish] generating consensus [=> ] 0.020773 s\r[racon::Polisher::polish] generating consensus [==> ] 0.021827 s\r[racon::Polisher::polish] generating consensus [===> ] 0.040910 s\r[racon::Polisher::polish] generating consensus [====> ] 0.041045 s\r[racon::Polisher::polish] generating consensus [=====> ] 0.051303 s\r[racon::Polisher::polish] generating consensus [======> ] 0.051497 s\r[racon::Polisher::polish] generating consensus [=======> ] 0.058868 s\r[racon::Polisher::polish] generating consensus [========> ] 0.058934 s\r[racon::Polisher::polish] generating consensus [=========> ] 0.068434 s\r[racon::Polisher::polish] generating consensus [==========> ] 0.068462 s\r[racon::Polisher::polish] generating consensus [===========> ] 0.086587 s\r[racon::Polisher::polish] generating consensus [============> ] 0.086614 s\r[racon::Polisher::polish] generating consensus [=============> ] 0.118306 s\r[racon::Polisher::polish] generating consensus [==============> ] 0.120215 s\r[racon::Polisher::polish] generating consensus [===============> ] 0.148133 s\r[racon::Polisher::polish] generating consensus [================> ] 0.160936 s\r[racon::Polisher::polish] generating consensus [=================> ] 0.173231 s\r[racon::Polisher::polish] generating consensus [==================> ] 0.173879 s\r[racon::Polisher::polish] generating consensus [===================>] 0.189225 s\r[racon::Polisher::polish] generating consensus [====================] 0.237113 s\n[racon::Polisher::] total = 0.365879 s\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": "2024-11-12 18:36:12", "plugin": "core", "name": "end_epoch", "raw_value": "1731436572.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 18:36:12", "plugin": "core", "name": "start_epoch", "raw_value": "1731436572.0000000"}, {"title": "Memory Allocated (MB)", "value": "38654", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "38654.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "racon/1.5.0+galaxy1-2", "has_data": true, "data": {"tool_id": "racon", "tool_version": "1.5.0+galaxy1", "test_index": 2, "time_seconds": 41.72891855239868, "inputs": {"reads": {"src": "hda", "id": "9fe03e3c39b07263"}, "overlaps": {"src": "hda", "id": "510dfb9c81301517"}, "corrected_reads": {"src": "hda", "id": "de1e9aada43893a1"}, "include_unpolished": false, "fragment_correction": false, "quality_threshold": "9.0", "no_trimming": true, "match": "7", "mismatch": "-4", "gap": "-3"}, "job": {"model_class": "Job", "id": "26e397a331032778", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T18:36:51.682337", "update_time": "2024-11-12T18:37:05.947812", "galaxy_version": "24.1", "external_id": "gxy-5g9jw", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/c/5/4/dataset_c542b339-c2a6-4a24-938f-5b29e04f0ac3.dat' reads.fasta && ln -s '/galaxy/server/database/objects/a/9/5/dataset_a9584baf-30ba-468a-b191-bfeaad77f8f7.dat' overlaps.sam && ln -s '/galaxy/server/database/objects/9/3/8/dataset_93896ef8-7e48-478a-8708-b081abb4bcfe.dat' corrected_reads.fasta && racon reads.fasta overlaps.sam corrected_reads.fasta -t ${GALAXY_SLOTS:-4} -w 500 -q 9.0 -e 0.3 --no-trimming -m 7 -x -4 -g -3 > racon_polished_consensus.fa", "user_email": "tests@fake.org", "command_version": "1.5.0", "params": {"include_unpolished": "false", "fragment_correction": "false", "window_length": "\"500\"", "quality_threshold": "\"9.0\"", "error_threshold": "\"0.3\"", "no_trimming": "true", "match": "\"7\"", "mismatch": "\"-4\"", "gap": "\"-3\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"corrected_reads": {"id": "de1e9aada43893a1", "src": "hda", "uuid": "93896ef8-7e48-478a-8708-b081abb4bcfe"}, "overlaps": {"id": "510dfb9c81301517", "src": "hda", "uuid": "a9584baf-30ba-468a-b191-bfeaad77f8f7"}, "reads": {"id": "9fe03e3c39b07263", "src": "hda", "uuid": "c542b339-c2a6-4a24-938f-5b29e04f0ac3"}}, "outputs": {"consensus": {"id": "26e397a331032778", "src": "hda", "uuid": "14e5cd0a-592c-488a-b820-66ac9bf410de"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[racon::Polisher::initialize] loaded target sequences 0.000842 s\n[racon::Polisher::initialize] loaded sequences 0.010392 s\n[racon::Polisher::initialize] loaded overlaps 0.011887 s\n[racon::Polisher::initialize] aligning overlaps [=> ] 0.002207 s\r[racon::Polisher::initialize] aligning overlaps [==> ] 0.002319 s\r[racon::Polisher::initialize] aligning overlaps [===> ] 0.002487 s\r[racon::Polisher::initialize] aligning overlaps [====> ] 0.002623 s\r[racon::Polisher::initialize] aligning overlaps [=====> ] 0.002689 s\r[racon::Polisher::initialize] aligning overlaps [======> ] 0.002762 s\r[racon::Polisher::initialize] aligning overlaps [=======> ] 0.002919 s\r[racon::Polisher::initialize] aligning overlaps [========> ] 0.003217 s\r[racon::Polisher::initialize] aligning overlaps [=========> ] 0.003304 s\r[racon::Polisher::initialize] aligning overlaps [==========> ] 0.003320 s\r[racon::Polisher::initialize] aligning overlaps [===========> ] 0.003426 s\r[racon::Polisher::initialize] aligning overlaps [============> ] 0.003551 s\r[racon::Polisher::initialize] aligning overlaps [=============> ] 0.003565 s\r[racon::Polisher::initialize] aligning overlaps [==============> ] 0.003666 s\r[racon::Polisher::initialize] aligning overlaps [===============> ] 0.003682 s\r[racon::Polisher::initialize] aligning overlaps [================> ] 0.003693 s\r[racon::Polisher::initialize] aligning overlaps [=================> ] 0.003705 s\r[racon::Polisher::initialize] aligning overlaps [==================> ] 0.003720 s\r[racon::Polisher::initialize] aligning overlaps [===================>] 0.003767 s\r[racon::Polisher::initialize] aligning overlaps [====================] 0.003782 s\n[racon::Polisher::initialize] transformed data into windows 0.000361 s\n[racon::Polisher::polish] generating consensus [=> ] 0.029112 s\r[racon::Polisher::polish] generating consensus [==> ] 0.032169 s\r[racon::Polisher::polish] generating consensus [===> ] 0.055828 s\r[racon::Polisher::polish] generating consensus [====> ] 0.055888 s\r[racon::Polisher::polish] generating consensus [=====> ] 0.066559 s\r[racon::Polisher::polish] generating consensus [======> ] 0.066617 s\r[racon::Polisher::polish] generating consensus [=======> ] 0.076605 s\r[racon::Polisher::polish] generating consensus [========> ] 0.076695 s\r[racon::Polisher::polish] generating consensus [=========> ] 0.087819 s\r[racon::Polisher::polish] generating consensus [==========> ] 0.090359 s\r[racon::Polisher::polish] generating consensus [===========> ] 0.108593 s\r[racon::Polisher::polish] generating consensus [============> ] 0.114878 s\r[racon::Polisher::polish] generating consensus [=============> ] 0.142685 s\r[racon::Polisher::polish] generating consensus [==============> ] 0.151782 s\r[racon::Polisher::polish] generating consensus [===============> ] 0.175327 s\r[racon::Polisher::polish] generating consensus [================> ] 0.180405 s\r[racon::Polisher::polish] generating consensus [=================> ] 0.201931 s\r[racon::Polisher::polish] generating consensus [==================> ] 0.201981 s\r[racon::Polisher::polish] generating consensus [===================>] 0.218374 s\r[racon::Polisher::polish] generating consensus [====================] 0.251099 s\n[racon::Polisher::] total = 0.281345 s\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[racon::Polisher::initialize] loaded target sequences 0.000842 s\n[racon::Polisher::initialize] loaded sequences 0.010392 s\n[racon::Polisher::initialize] loaded overlaps 0.011887 s\n[racon::Polisher::initialize] aligning overlaps [=> ] 0.002207 s\r[racon::Polisher::initialize] aligning overlaps [==> ] 0.002319 s\r[racon::Polisher::initialize] aligning overlaps [===> ] 0.002487 s\r[racon::Polisher::initialize] aligning overlaps [====> ] 0.002623 s\r[racon::Polisher::initialize] aligning overlaps [=====> ] 0.002689 s\r[racon::Polisher::initialize] aligning overlaps [======> ] 0.002762 s\r[racon::Polisher::initialize] aligning overlaps [=======> ] 0.002919 s\r[racon::Polisher::initialize] aligning overlaps [========> ] 0.003217 s\r[racon::Polisher::initialize] aligning overlaps [=========> ] 0.003304 s\r[racon::Polisher::initialize] aligning overlaps [==========> ] 0.003320 s\r[racon::Polisher::initialize] aligning overlaps [===========> ] 0.003426 s\r[racon::Polisher::initialize] aligning overlaps [============> ] 0.003551 s\r[racon::Polisher::initialize] aligning overlaps [=============> ] 0.003565 s\r[racon::Polisher::initialize] aligning overlaps [==============> ] 0.003666 s\r[racon::Polisher::initialize] aligning overlaps [===============> ] 0.003682 s\r[racon::Polisher::initialize] aligning overlaps [================> ] 0.003693 s\r[racon::Polisher::initialize] aligning overlaps [=================> ] 0.003705 s\r[racon::Polisher::initialize] aligning overlaps [==================> ] 0.003720 s\r[racon::Polisher::initialize] aligning overlaps [===================>] 0.003767 s\r[racon::Polisher::initialize] aligning overlaps [====================] 0.003782 s\n[racon::Polisher::initialize] transformed data into windows 0.000361 s\n[racon::Polisher::polish] generating consensus [=> ] 0.029112 s\r[racon::Polisher::polish] generating consensus [==> ] 0.032169 s\r[racon::Polisher::polish] generating consensus [===> ] 0.055828 s\r[racon::Polisher::polish] generating consensus [====> ] 0.055888 s\r[racon::Polisher::polish] generating consensus [=====> ] 0.066559 s\r[racon::Polisher::polish] generating consensus [======> ] 0.066617 s\r[racon::Polisher::polish] generating consensus [=======> ] 0.076605 s\r[racon::Polisher::polish] generating consensus [========> ] 0.076695 s\r[racon::Polisher::polish] generating consensus [=========> ] 0.087819 s\r[racon::Polisher::polish] generating consensus [==========> ] 0.090359 s\r[racon::Polisher::polish] generating consensus [===========> ] 0.108593 s\r[racon::Polisher::polish] generating consensus [============> ] 0.114878 s\r[racon::Polisher::polish] generating consensus [=============> ] 0.142685 s\r[racon::Polisher::polish] generating consensus [==============> ] 0.151782 s\r[racon::Polisher::polish] generating consensus [===============> ] 0.175327 s\r[racon::Polisher::polish] generating consensus [================> ] 0.180405 s\r[racon::Polisher::polish] generating consensus [=================> ] 0.201931 s\r[racon::Polisher::polish] generating consensus [==================> ] 0.201981 s\r[racon::Polisher::polish] generating consensus [===================>] 0.218374 s\r[racon::Polisher::polish] generating consensus [====================] 0.251099 s\n[racon::Polisher::] total = 0.281345 s\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": "2024-11-12 18:36:53", "plugin": "core", "name": "end_epoch", "raw_value": "1731436613.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 18:36:53", "plugin": "core", "name": "start_epoch", "raw_value": "1731436613.0000000"}, {"title": "Memory Allocated (MB)", "value": "38654", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "38654.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "samtools_idxstats/2.0.5-0", "has_data": true, "data": {"tool_id": "samtools_idxstats", "tool_version": "2.0.5", "test_index": 0, "time_seconds": 40.50754189491272, "inputs": {"input": {"src": "hda", "id": "e28001cc42f670cf"}}, "job": {"model_class": "Job", "id": "aa586026ef3fa7da", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:02:12.835593", "update_time": "2024-11-12T19:02:30.608845", "galaxy_version": "24.1", "external_id": "gxy-pkrw9", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/8/e/4/dataset_8e492759-30ce-4e71-af4c-514bb13db9ff.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/1/5/7/metadata_157e61ef-f442-4f7f-b121-5c1ce21ed97d.dat' infile.bai && samtools idxstats -@ $addthreads infile > '/galaxy/server/database/objects/b/1/6/dataset_b16d5d5d-2e67-4e58-a412-33a26efd484d.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.16)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input": {"id": "e28001cc42f670cf", "src": "hda", "uuid": "8e492759-30ce-4e71-af4c-514bb13db9ff"}}, "outputs": {"output": {"id": "300354dbb5b5c093", "src": "hda", "uuid": "b16d5d5d-2e67-4e58-a412-33a26efd484d"}}, "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": "2024-11-12 19:02:18", "plugin": "core", "name": "end_epoch", "raw_value": "1731438138.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:02:18", "plugin": "core", "name": "start_epoch", "raw_value": "1731438138.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "samtools_idxstats/2.0.5-0", "has_data": true, "data": {"tool_id": "samtools_idxstats", "tool_version": "2.0.5", "test_index": 0, "time_seconds": 38.238502979278564, "inputs": {"input": {"src": "hda", "id": "e9017cc4c50081f6"}}, "job": {"model_class": "Job", "id": "ab93220ba3f66e53", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:03:33.222765", "update_time": "2024-11-12T19:03:48.123256", "galaxy_version": "24.1", "external_id": "gxy-c6tz9", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/9/4/6/dataset_9466916e-bdbc-4274-aae8-c814ae658f25.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/6/2/e/metadata_62efc044-623b-4dfb-aaef-05bb736b0341.dat' infile.bai && samtools idxstats -@ $addthreads infile > '/galaxy/server/database/objects/7/3/9/dataset_73996f97-d114-4b84-94b6-7d99a0ca7aa4.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.16)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input": {"id": "e9017cc4c50081f6", "src": "hda", "uuid": "9466916e-bdbc-4274-aae8-c814ae658f25"}}, "outputs": {"output": {"id": "6159239c70dfe0e3", "src": "hda", "uuid": "73996f97-d114-4b84-94b6-7d99a0ca7aa4"}}, "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": "2024-11-12 19:03:35", "plugin": "core", "name": "end_epoch", "raw_value": "1731438215.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:03:35", "plugin": "core", "name": "start_epoch", "raw_value": "1731438215.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "samtools_idxstats/2.0.5-1", "has_data": true, "data": {"tool_id": "samtools_idxstats", "tool_version": "2.0.5", "test_index": 1, "time_seconds": 38.28343605995178, "inputs": {"input": {"src": "hda", "id": "02c51e0fd94b8db2"}}, "job": {"model_class": "Job", "id": "a042cd357bab67bc", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:02:54.032399", "update_time": "2024-11-12T19:03:08.877382", "galaxy_version": "24.1", "external_id": "gxy-q2p79", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/0/e/f/dataset_0ef29726-5e71-4ce0-9fe8-a6a82a0ca4a3.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/2/3/6/metadata_236ca541-8c99-4b11-88b7-ddd1cb99d66b.dat' infile.bai && samtools idxstats -@ $addthreads infile > '/galaxy/server/database/objects/4/2/0/dataset_42025539-b06b-4944-8295-04d38befd385.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.16)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input": {"id": "02c51e0fd94b8db2", "src": "hda", "uuid": "0ef29726-5e71-4ce0-9fe8-a6a82a0ca4a3"}}, "outputs": {"output": {"id": "22091d51ce4ba6bc", "src": "hda", "uuid": "42025539-b06b-4944-8295-04d38befd385"}}, "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": "2024-11-12 19:02:56", "plugin": "core", "name": "end_epoch", "raw_value": "1731438176.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:02:56", "plugin": "core", "name": "start_epoch", "raw_value": "1731438176.0000000"}, {"title": "Memory Allocated (MB)", "value": "8160", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "8160.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "samtools_idxstats/2.0.5-1", "has_data": true, "data": {"tool_id": "samtools_idxstats", "tool_version": "2.0.5", "test_index": 1, "time_seconds": 36.31574320793152, "inputs": {"input": {"src": "hda", "id": "2835e793c6229866"}}, "job": {"model_class": "Job", "id": "e19a2a42d2c77e5c", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:04:09.644155", "update_time": "2024-11-12T19:04:24.358948", "galaxy_version": "24.1", "external_id": "gxy-mx84h", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/a/6/1/dataset_a612509c-8cc2-4b67-973c-77010d62e2a5.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/1/4/e/metadata_14e4b6d3-5fc6-4939-989f-9b04bf1857b6.dat' infile.bai && samtools idxstats -@ $addthreads infile > '/galaxy/server/database/objects/a/a/3/dataset_aa3f1448-bdd8-474f-ac1c-2e34b6eadbf4.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.16)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input": {"id": "2835e793c6229866", "src": "hda", "uuid": "a612509c-8cc2-4b67-973c-77010d62e2a5"}}, "outputs": {"output": {"id": "a00ca2bfd48719ce", "src": "hda", "uuid": "aa3f1448-bdd8-474f-ac1c-2e34b6eadbf4"}}, "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": "2024-11-12 19:04:12", "plugin": "core", "name": "end_epoch", "raw_value": "1731438252.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:04:12", "plugin": "core", "name": "start_epoch", "raw_value": "1731438252.0000000"}, {"title": "Memory Allocated (MB)", "value": 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76.83302545547485, "inputs": {"input_loom": {"src": "hda", "id": "6867bd8d18961a91"}, "colour_by": "Treatment", "shape_by": "Mutation_Status"}, "job": {"model_class": "Job", "id": "a00ca2bfd48719ce", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.22.0", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:16:23.323628", "update_time": "2024-11-12T19:17:19.005509", "galaxy_version": "24.1", "external_id": "gxy-m4pd8", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/c99ba278dfa9/scater_plot_pca/scater-plot-pca.R' -i '/galaxy/server/database/objects/7/8/1/dataset_78182ace-7487-4898-b891-1558963a2ec3.dat' --colour-by 'Treatment' --shape-by 'Mutation_Status' -o '/galaxy/server/database/objects/0/d/8/dataset_0d8f98be-ceee-4d4a-abb0-5ced5f270295.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "shape_by": "\"Mutation_Status\"", "size_by": null, "colour_by": "\"Treatment\""}, "inputs": {"input_loom": {"id": "6867bd8d18961a91", "src": "hda", "uuid": "78182ace-7487-4898-b891-1558963a2ec3"}}, "outputs": {"output_plot": {"id": "8843a2185980b4b9", "src": "hda", "uuid": "0d8f98be-ceee-4d4a-abb0-5ced5f270295"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Loading required package: S4Vectors\nLoading required package: stats4\nLoading required package: BiocGenerics\n\nAttaching package: \u2018BiocGenerics\u2019\n\nThe following objects are masked from \u2018package:stats\u2019:\n\n IQR, mad, sd, var, xtabs\n\nThe following objects are masked from \u2018package:base\u2019:\n\n anyDuplicated, append, as.data.frame, basename, cbind, colnames,\n dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,\n grepl, 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colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,\n colWeightedMeans, colWeightedMedians, colWeightedSds,\n colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,\n rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,\n rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,\n rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,\n rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,\n rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,\n rowWeightedMads, rowWeightedMeans, rowWeightedMedians,\n rowWeightedSds, rowWeightedVars\n\nLoading required package: GenomicRanges\nLoading required package: IRanges\nLoading required package: GenomeInfoDb\nLoading required package: Biobase\nWelcome to Bioconductor\n\n Vignettes contain introductory material; view with\n 'browseVignettes()'. To cite Bioconductor, see\n 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\n\nAttaching package: \u2018Biobase\u2019\n\nThe following object is masked from \u2018package:MatrixGenerics\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n anyMissing, rowMedians\n\nLoading required package: rhdf5\nLoading required package: BiocIO\nLoading required package: scuttle\nLoading required package: ggplot2\nWarning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, :\n You're computing too large a percentage of total singular values, use a standard svd instead.\nWarning message:\nIn check_numbers(k = k, nu = nu, nv = nv, limit = min(dim(x)) - :\n more singular values/vectors requested than available\nSaving 7 x 7 in image\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Loading required package: S4Vectors\nLoading required package: stats4\nLoading required package: BiocGenerics\n\nAttaching package: \u2018BiocGenerics\u2019\n\nThe following objects are masked from \u2018package:stats\u2019:\n\n IQR, mad, sd, var, xtabs\n\nThe following objects are masked from \u2018package:base\u2019:\n\n anyDuplicated, append, as.data.frame, basename, cbind, colnames,\n dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,\n grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,\n order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\n rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,\n union, unique, unsplit, which.max, which.min\n\n\nAttaching package: \u2018S4Vectors\u2019\n\nThe following objects are masked from \u2018package:base\u2019:\n\n expand.grid, I, unname\n\nLoading required package: SingleCellExperiment\nLoading required package: SummarizedExperiment\nLoading required package: MatrixGenerics\nLoading required package: matrixStats\n\nAttaching package: \u2018MatrixGenerics\u2019\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,\n colCounts, colCummaxs, colCummins, colCumprods, colCumsums,\n colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,\n colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,\n colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,\n colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,\n colWeightedMeans, colWeightedMedians, colWeightedSds,\n colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,\n rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,\n rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,\n rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,\n rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,\n rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,\n rowWeightedMads, rowWeightedMeans, rowWeightedMedians,\n rowWeightedSds, rowWeightedVars\n\nLoading required package: GenomicRanges\nLoading required package: IRanges\nLoading required package: GenomeInfoDb\nLoading required package: Biobase\nWelcome to Bioconductor\n\n Vignettes contain introductory material; view with\n 'browseVignettes()'. To cite Bioconductor, see\n 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\n\nAttaching package: \u2018Biobase\u2019\n\nThe following object is masked from \u2018package:MatrixGenerics\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n anyMissing, rowMedians\n\nLoading required package: rhdf5\nLoading required package: BiocIO\nLoading required package: scuttle\nLoading required package: ggplot2\nWarning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, :\n You're computing too large a percentage of total singular values, use a standard svd instead.\nWarning message:\nIn check_numbers(k = k, nu = nu, nv = nv, limit = min(dim(x)) - :\n more singular values/vectors requested than available\nSaving 7 x 7 in image\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "12 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": 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which.min\n\n\nAttaching package: \u2018S4Vectors\u2019\n\nThe following objects are masked from \u2018package:base\u2019:\n\n expand.grid, I, unname\n\nLoading required package: SingleCellExperiment\nLoading required package: SummarizedExperiment\nLoading required package: MatrixGenerics\nLoading required package: matrixStats\n\nAttaching package: \u2018MatrixGenerics\u2019\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,\n colCounts, colCummaxs, colCummins, colCumprods, colCumsums,\n colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,\n colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,\n colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,\n colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,\n colWeightedMeans, colWeightedMedians, colWeightedSds,\n colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,\n rowCollapse, rowCounts, rowCummaxs, 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To cite Bioconductor, see\n 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\n\nAttaching package: \u2018Biobase\u2019\n\nThe following object is masked from \u2018package:MatrixGenerics\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n anyMissing, rowMedians\n\nLoading required package: rhdf5\nLoading required package: BiocIO\nLoading required package: scuttle\nLoading required package: ggplot2\nWarning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, :\n You're computing too large a percentage of total singular values, use a standard svd instead.\nWarning message:\nIn check_numbers(k = k, nu = nu, nv = nv, limit = min(dim(x)) - :\n more singular values/vectors requested than available\nSaving 7 x 7 in image\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Loading required package: S4Vectors\nLoading required package: stats4\nLoading required package: BiocGenerics\n\nAttaching package: \u2018BiocGenerics\u2019\n\nThe following objects are masked from \u2018package:stats\u2019:\n\n IQR, mad, sd, var, xtabs\n\nThe following objects are masked from \u2018package:base\u2019:\n\n anyDuplicated, append, as.data.frame, basename, cbind, colnames,\n dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,\n grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,\n order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\n rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,\n union, unique, unsplit, which.max, which.min\n\n\nAttaching package: \u2018S4Vectors\u2019\n\nThe following objects are masked from \u2018package:base\u2019:\n\n expand.grid, I, unname\n\nLoading required package: SingleCellExperiment\nLoading required package: SummarizedExperiment\nLoading required package: MatrixGenerics\nLoading required package: matrixStats\n\nAttaching package: \u2018MatrixGenerics\u2019\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,\n colCounts, colCummaxs, colCummins, colCumprods, colCumsums,\n colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,\n colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,\n colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,\n colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,\n colWeightedMeans, colWeightedMedians, colWeightedSds,\n colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,\n rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,\n rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,\n rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,\n rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,\n rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,\n rowWeightedMads, rowWeightedMeans, rowWeightedMedians,\n rowWeightedSds, rowWeightedVars\n\nLoading required package: GenomicRanges\nLoading required package: IRanges\nLoading required package: GenomeInfoDb\nLoading required package: Biobase\nWelcome to Bioconductor\n\n Vignettes contain introductory material; view with\n 'browseVignettes()'. To cite Bioconductor, see\n 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\n\nAttaching package: \u2018Biobase\u2019\n\nThe following object is masked from \u2018package:MatrixGenerics\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n anyMissing, rowMedians\n\nLoading required package: rhdf5\nLoading required package: BiocIO\nLoading required package: scuttle\nLoading required package: ggplot2\nWarning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, :\n You're computing too large a percentage of total singular values, use a standard svd instead.\nWarning message:\nIn check_numbers(k = k, nu = nu, nv = nv, limit = min(dim(x)) - :\n more singular values/vectors requested than available\nSaving 7 x 7 in image\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "11 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "11.0000000"}, {"title": "Job End Time", "value": "2024-11-12 19:17:54", "plugin": "core", "name": "end_epoch", "raw_value": "1731439074.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:17:43", "plugin": "core", "name": "start_epoch", "raw_value": "1731439063.0000000"}, {"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": "sniffles/1.0.12+galaxy0-0", "has_data": true, "data": {"tool_id": "sniffles", "tool_version": "1.0.12+galaxy0", "test_index": 0, "time_seconds": 40.543813943862915, "inputs": {"input": {"src": "hda", "id": "723660a468bc344b"}}, "job": {"model_class": "Job", "id": "d7a8c3e6bbd352d3", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:19:16.275452", "update_time": "2024-11-12T19:19:34.223322", "galaxy_version": "24.1", "external_id": "gxy-7v9rl", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/4/2/7/dataset_4279e85e-8292-41d2-9ac4-861bf53aac30.dat' input.bam && ln -f -s '/galaxy/server/database/objects/_metadata_files/a/d/4/metadata_ad417556-90f0-49f3-ae5c-643aabbe79dc.dat' input.bam.bai && sniffles -t ${GALAXY_SLOTS:-2} -m 'input.bam' -v '/galaxy/server/database/objects/3/5/2/dataset_3529eaba-882b-40af-8fce-410727ec3c0c.dat' --min_support 10 --max_num_splits 7 --max_distance 1000 --min_length 30 --minmapping_qual 20 --num_reads_report 0 --min_zmw 0 --cluster_support 1 --allelefreq 0.0 --min_homo_af 0.8 --min_het_af 0.3 --del_ratio 0.0458369 --ins_ratio 0.049379 --max_diff_per_window 50 --max_dist_aln_events 4", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "parameter_estimation_options": "{\"del_ratio\": \"0.0458369\", \"ins_ratio\": \"0.049379\", \"max_diff_per_window\": \"50\", \"max_dist_aln_events\": \"4\", \"skip_parameter_estimation\": false}", "advanced_options": "{\"ccs_reads\": false, \"ignore_sd\": false, \"not_report_seq\": false, \"report_BND\": false}", "clustering_options": "{\"allelefreq\": \"0.0\", \"cluster\": false, \"cluster_support\": \"1\", \"min_het_af\": \"0.3\", \"min_homo_af\": \"0.8\"}", "general_options": "{\"cs_string\": false, \"max_distance\": \"1000\", \"max_num_splits\": \"7\", \"min_length\": \"30\", \"min_seq_size\": \"\", \"min_support\": \"10\", \"min_zmw\": \"0\", \"minmapping_qual\": \"20\", \"num_reads_report\": \"0\"}"}, "inputs": {"input": {"id": "723660a468bc344b", "src": "hda", "uuid": "4279e85e-8292-41d2-9ac4-861bf53aac30"}}, "outputs": {"output": {"id": "c9b91d921d105b73", "src": "hda", "uuid": "3529eaba-882b-40af-8fce-410727ec3c0c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Estimating parameter...\n\tMax dist between aln events: 4\n\tMax diff in window: 50\n\tMin score ratio: 2\n\tAvg DEL ratio: 0.0432235\n\tAvg INS ratio: 0.0740733\nStart parsing... 21\n\tSwitch Chr 21\n\t\tReassessing breakpoints\n\t\tContinue parsing\n\tFinalizing ..\nStart genotype calling:\n\tReopening Bam file for parsing coverage \n\tFinalizing ..\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Estimating parameter...\n\tMax dist between aln events: 4\n\tMax diff in window: 50\n\tMin score ratio: 2\n\tAvg DEL ratio: 0.0432235\n\tAvg INS ratio: 0.0740733\nStart parsing... 21\n\tSwitch Chr 21\n\t\tReassessing breakpoints\n\t\tContinue parsing\n\tFinalizing ..\nStart genotype calling:\n\tReopening Bam file for parsing coverage \n\tFinalizing ..\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-12 19:19:21", "plugin": "core", "name": "end_epoch", "raw_value": "1731439161.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:19:20", "plugin": "core", "name": "start_epoch", "raw_value": "1731439160.0000000"}, {"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": "sniffles/1.0.12+galaxy0-1", "has_data": true, "data": {"tool_id": "sniffles", "tool_version": "1.0.12+galaxy0", "test_index": 1, "time_seconds": 37.6736741065979, "inputs": {"input": {"src": "hda", "id": "494884f45600f3fa"}, "general_options|num_reads_report": "-1"}, "job": {"model_class": "Job", "id": "3afdcc1316e79fd7", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:19:56.794445", "update_time": "2024-11-12T19:20:11.838903", "galaxy_version": "24.1", "external_id": "gxy-62pn5", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/d/f/5/dataset_df57fb7a-7822-4099-80ec-d4cdebab4b9d.dat' input.bam && ln -f -s '/galaxy/server/database/objects/_metadata_files/9/f/1/metadata_9f17ed6c-a130-4dfe-96e4-819c22011d8b.dat' input.bam.bai && sniffles -t ${GALAXY_SLOTS:-2} -m 'input.bam' -v '/galaxy/server/database/objects/f/8/e/dataset_f8e5edcf-6bcc-40ac-9384-e021c8c3b00d.dat' --min_support 10 --max_num_splits 7 --max_distance 1000 --min_length 30 --minmapping_qual 20 --num_reads_report -1 --min_zmw 0 --cluster_support 1 --allelefreq 0.0 --min_homo_af 0.8 --min_het_af 0.3 --del_ratio 0.0458369 --ins_ratio 0.049379 --max_diff_per_window 50 --max_dist_aln_events 4", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "parameter_estimation_options": "{\"del_ratio\": \"0.0458369\", \"ins_ratio\": \"0.049379\", \"max_diff_per_window\": \"50\", \"max_dist_aln_events\": \"4\", \"skip_parameter_estimation\": false}", "advanced_options": "{\"ccs_reads\": false, \"ignore_sd\": false, \"not_report_seq\": false, \"report_BND\": false}", "clustering_options": "{\"allelefreq\": \"0.0\", \"cluster\": false, \"cluster_support\": \"1\", \"min_het_af\": \"0.3\", \"min_homo_af\": \"0.8\"}", "general_options": "{\"cs_string\": false, \"max_distance\": \"1000\", \"max_num_splits\": \"7\", \"min_length\": \"30\", \"min_seq_size\": \"\", \"min_support\": \"10\", \"min_zmw\": \"0\", \"minmapping_qual\": \"20\", \"num_reads_report\": \"-1\"}"}, "inputs": {"input": {"id": "494884f45600f3fa", "src": "hda", "uuid": "df57fb7a-7822-4099-80ec-d4cdebab4b9d"}}, "outputs": {"output": {"id": "6521c6a01a09c7e3", "src": "hda", "uuid": "f8e5edcf-6bcc-40ac-9384-e021c8c3b00d"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Estimating parameter...\n\tMax dist between aln events: 4\n\tMax diff in window: 50\n\tMin score ratio: 2\n\tAvg DEL ratio: 0.0432235\n\tAvg INS ratio: 0.0740733\nStart parsing... 21\n\tSwitch Chr 21\n\t\tReassessing breakpoints\n\t\tContinue parsing\n\tFinalizing ..\nStart genotype calling:\n\tReopening Bam file for parsing coverage \n\tFinalizing ..\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Estimating parameter...\n\tMax dist between aln events: 4\n\tMax diff in window: 50\n\tMin score ratio: 2\n\tAvg DEL ratio: 0.0432235\n\tAvg INS ratio: 0.0740733\nStart parsing... 21\n\tSwitch Chr 21\n\t\tReassessing breakpoints\n\t\tContinue parsing\n\tFinalizing ..\nStart genotype calling:\n\tReopening Bam file for parsing coverage \n\tFinalizing ..\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": "2024-11-12 19:19:58", "plugin": "core", "name": "end_epoch", "raw_value": "1731439198.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:19:58", "plugin": "core", "name": "start_epoch", "raw_value": "1731439198.0000000"}, {"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": "sniffles/1.0.12+galaxy0-2", "has_data": true, "data": {"tool_id": "sniffles", "tool_version": "1.0.12+galaxy0", "test_index": 2, "time_seconds": 35.828497886657715, "inputs": {"input": {"src": "hda", "id": "235090b52faed188"}, "general_options|cs_string": true}, "job": {"model_class": "Job", "id": "a9f5e69b88d408bc", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:20:34.289656", "update_time": "2024-11-12T19:20:47.853161", "galaxy_version": "24.1", "external_id": "gxy-pmj5l", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/3/4/8/dataset_3483f991-258c-48d6-808e-6b1007e8bc4b.dat' input.bam && ln -f -s '/galaxy/server/database/objects/_metadata_files/0/7/0/metadata_070aa559-4582-4ce6-8c96-e06478a18363.dat' input.bam.bai && sniffles -t ${GALAXY_SLOTS:-2} -m 'input.bam' -v '/galaxy/server/database/objects/e/6/d/dataset_e6d8bf90-2c24-4f71-be0a-3882e8acacdd.dat' --min_support 10 --max_num_splits 7 --max_distance 1000 --min_length 30 --minmapping_qual 20 --num_reads_report 0 --min_zmw 0 --cs_string --cluster_support 1 --allelefreq 0.0 --min_homo_af 0.8 --min_het_af 0.3 --del_ratio 0.0458369 --ins_ratio 0.049379 --max_diff_per_window 50 --max_dist_aln_events 4", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "parameter_estimation_options": "{\"del_ratio\": \"0.0458369\", \"ins_ratio\": \"0.049379\", \"max_diff_per_window\": \"50\", \"max_dist_aln_events\": \"4\", \"skip_parameter_estimation\": false}", "advanced_options": "{\"ccs_reads\": false, \"ignore_sd\": false, \"not_report_seq\": false, \"report_BND\": false}", "clustering_options": "{\"allelefreq\": \"0.0\", \"cluster\": false, \"cluster_support\": \"1\", \"min_het_af\": \"0.3\", \"min_homo_af\": \"0.8\"}", "general_options": "{\"cs_string\": true, \"max_distance\": \"1000\", \"max_num_splits\": \"7\", \"min_length\": \"30\", \"min_seq_size\": \"\", \"min_support\": \"10\", \"min_zmw\": \"0\", \"minmapping_qual\": \"20\", \"num_reads_report\": \"0\"}"}, "inputs": {"input": {"id": "235090b52faed188", "src": "hda", "uuid": "3483f991-258c-48d6-808e-6b1007e8bc4b"}}, "outputs": {"output": {"id": "1fd45311be778b92", "src": "hda", "uuid": "e6d8bf90-2c24-4f71-be0a-3882e8acacdd"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Estimating parameter...\n\tMax dist between aln events: 4\n\tMax diff in window: 50\n\tMin score ratio: 2\n\tAvg DEL ratio: 0.0432235\n\tAvg INS ratio: 0.0740733\nStart parsing... 21\n\tSwitch Chr 21\n\t\tReassessing breakpoints\n\t\tContinue parsing\n\tFinalizing ..\nStart genotype calling:\n\tReopening Bam file for parsing coverage \n\tFinalizing ..\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Estimating parameter...\n\tMax dist between aln events: 4\n\tMax diff in window: 50\n\tMin score ratio: 2\n\tAvg DEL ratio: 0.0432235\n\tAvg INS ratio: 0.0740733\nStart parsing... 21\n\tSwitch Chr 21\n\t\tReassessing breakpoints\n\t\tContinue parsing\n\tFinalizing ..\nStart genotype calling:\n\tReopening Bam file for parsing coverage \n\tFinalizing ..\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": "2024-11-12 19:20:36", "plugin": "core", "name": "end_epoch", "raw_value": "1731439236.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:20:36", "plugin": "core", "name": "start_epoch", "raw_value": "1731439236.0000000"}, {"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": "sniffles/1.0.12+galaxy0-3", "has_data": true, "data": {"tool_id": "sniffles", "tool_version": "1.0.12+galaxy0", "test_index": 3, "time_seconds": 36.372336626052856, "inputs": {"input": {"src": "hda", "id": "f53da835c149b5d4"}, "clustering_options|cluster": true}, "job": {"model_class": "Job", "id": "c6e0259b7027cf38", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:21:10.397668", "update_time": "2024-11-12T19:21:24.205776", "galaxy_version": "24.1", "external_id": "gxy-89zz8", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/5/a/3/dataset_5a345489-d0d7-4c1a-a7ff-bf3f5b842a7e.dat' input.bam && ln -f -s '/galaxy/server/database/objects/_metadata_files/7/0/6/metadata_706794ce-f20f-4ba7-8be9-a0f21410e95a.dat' input.bam.bai && sniffles -t ${GALAXY_SLOTS:-2} -m 'input.bam' -v '/galaxy/server/database/objects/a/4/7/dataset_a47ba7ce-d694-44d9-a221-42d617c1db16.dat' --min_support 10 --max_num_splits 7 --max_distance 1000 --min_length 30 --minmapping_qual 20 --num_reads_report 0 --min_zmw 0 --cluster --cluster_support 1 --allelefreq 0.0 --min_homo_af 0.8 --min_het_af 0.3 --del_ratio 0.0458369 --ins_ratio 0.049379 --max_diff_per_window 50 --max_dist_aln_events 4", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "parameter_estimation_options": "{\"del_ratio\": \"0.0458369\", \"ins_ratio\": \"0.049379\", \"max_diff_per_window\": \"50\", \"max_dist_aln_events\": \"4\", \"skip_parameter_estimation\": false}", "advanced_options": "{\"ccs_reads\": false, \"ignore_sd\": false, \"not_report_seq\": false, \"report_BND\": false}", "clustering_options": "{\"allelefreq\": \"0.0\", \"cluster\": true, \"cluster_support\": \"1\", \"min_het_af\": \"0.3\", \"min_homo_af\": \"0.8\"}", "general_options": "{\"cs_string\": false, \"max_distance\": \"1000\", \"max_num_splits\": \"7\", \"min_length\": \"30\", \"min_seq_size\": \"\", \"min_support\": \"10\", \"min_zmw\": \"0\", \"minmapping_qual\": \"20\", \"num_reads_report\": \"0\"}"}, "inputs": {"input": {"id": "f53da835c149b5d4", "src": "hda", "uuid": "5a345489-d0d7-4c1a-a7ff-bf3f5b842a7e"}}, "outputs": {"output": {"id": "8282889456266094", "src": "hda", "uuid": "a47ba7ce-d694-44d9-a221-42d617c1db16"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Estimating parameter...\n\tMax dist between aln events: 4\n\tMax diff in window: 50\n\tMin score ratio: 2\n\tAvg DEL ratio: 0.0432235\n\tAvg INS ratio: 0.0740733\nStart parsing... 21\n\tSwitch Chr 21\n\t\tReassessing breakpoints\n\t\tContinue parsing\n\tFinalizing ..\nStart phasing: \n\tCleaning tmp files\nStart genotype calling:\n\tReopening Bam file for parsing coverage \n\tFinalizing ..\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Estimating parameter...\n\tMax dist between aln events: 4\n\tMax diff in window: 50\n\tMin score ratio: 2\n\tAvg DEL ratio: 0.0432235\n\tAvg INS ratio: 0.0740733\nStart parsing... 21\n\tSwitch Chr 21\n\t\tReassessing breakpoints\n\t\tContinue parsing\n\tFinalizing ..\nStart phasing: \n\tCleaning tmp files\nStart genotype calling:\n\tReopening Bam file for parsing coverage \n\tFinalizing ..\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": "2024-11-12 19:21:12", "plugin": "core", "name": "end_epoch", "raw_value": "1731439272.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:21:12", "plugin": "core", "name": "start_epoch", "raw_value": "1731439272.0000000"}, {"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": "sniffles/1.0.12+galaxy0-4", "has_data": true, "data": {"tool_id": "sniffles", "tool_version": "1.0.12+galaxy0", "test_index": 4, "time_seconds": 36.36087703704834, "inputs": {"input": {"src": "hda", "id": "f98c7ea3cf6a561f"}, "advanced_options|report_BND": true}, "job": {"model_class": "Job", "id": "2d1ef22cada24364", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:21:46.516974", "update_time": "2024-11-12T19:22:00.475785", "galaxy_version": "24.1", "external_id": "gxy-7zbmm", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/d/2/2/dataset_d2288b3c-4fed-4d18-957f-78901b560570.dat' input.bam && ln -f -s '/galaxy/server/database/objects/_metadata_files/a/4/2/metadata_a421b58d-e1e0-43b3-ae23-0ea7243fae7d.dat' input.bam.bai && sniffles -t ${GALAXY_SLOTS:-2} -m 'input.bam' -v '/galaxy/server/database/objects/9/c/0/dataset_9c0ff8d6-b30c-4d3b-a9eb-0926236992c9.dat' --min_support 10 --max_num_splits 7 --max_distance 1000 --min_length 30 --minmapping_qual 20 --num_reads_report 0 --min_zmw 0 --cluster_support 1 --allelefreq 0.0 --min_homo_af 0.8 --min_het_af 0.3 --report_BND --del_ratio 0.0458369 --ins_ratio 0.049379 --max_diff_per_window 50 --max_dist_aln_events 4", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "parameter_estimation_options": "{\"del_ratio\": \"0.0458369\", \"ins_ratio\": \"0.049379\", \"max_diff_per_window\": \"50\", \"max_dist_aln_events\": \"4\", \"skip_parameter_estimation\": false}", "advanced_options": "{\"ccs_reads\": false, \"ignore_sd\": false, \"not_report_seq\": false, \"report_BND\": true}", "clustering_options": "{\"allelefreq\": \"0.0\", \"cluster\": false, \"cluster_support\": \"1\", \"min_het_af\": \"0.3\", \"min_homo_af\": \"0.8\"}", "general_options": "{\"cs_string\": false, \"max_distance\": \"1000\", \"max_num_splits\": \"7\", \"min_length\": \"30\", \"min_seq_size\": \"\", \"min_support\": \"10\", \"min_zmw\": \"0\", \"minmapping_qual\": \"20\", \"num_reads_report\": \"0\"}"}, "inputs": {"input": {"id": "f98c7ea3cf6a561f", "src": "hda", "uuid": "d2288b3c-4fed-4d18-957f-78901b560570"}}, "outputs": {"output": {"id": "26a32c328603d720", "src": "hda", "uuid": "9c0ff8d6-b30c-4d3b-a9eb-0926236992c9"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Estimating parameter...\n\tMax dist between aln events: 4\n\tMax diff in window: 50\n\tMin score ratio: 2\n\tAvg DEL ratio: 0.0432235\n\tAvg INS ratio: 0.0740733\nStart parsing... 21\n\tSwitch Chr 21\n\t\tReassessing breakpoints\n\t\tContinue parsing\n\tFinalizing ..\nStart genotype calling:\n\tReopening Bam file for parsing coverage \n\tFinalizing ..\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Estimating parameter...\n\tMax dist between aln events: 4\n\tMax diff in window: 50\n\tMin score ratio: 2\n\tAvg DEL ratio: 0.0432235\n\tAvg INS ratio: 0.0740733\nStart parsing... 21\n\tSwitch Chr 21\n\t\tReassessing breakpoints\n\t\tContinue parsing\n\tFinalizing ..\nStart genotype calling:\n\tReopening Bam file for parsing coverage \n\tFinalizing ..\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": "2024-11-12 19:21:47", "plugin": "core", "name": "end_epoch", "raw_value": "1731439307.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:21:47", "plugin": "core", "name": "start_epoch", "raw_value": "1731439307.0000000"}, {"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": "sniffles/1.0.12+galaxy0-5", "has_data": true, "data": {"tool_id": "sniffles", "tool_version": "1.0.12+galaxy0", "test_index": 5, "time_seconds": 37.33622431755066, "inputs": {"input": {"src": "hda", "id": "986140a6d7d4b492"}, "parameter_estimation_options|skip_parameter_estimation": true}, "job": {"model_class": "Job", "id": "bef9ef82cea6186b", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-11-12T19:22:22.962070", "update_time": "2024-11-12T19:22:37.976207", "galaxy_version": "24.1", "external_id": "gxy-jf26h", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/d/4/8/dataset_d485f910-578b-4daf-b4d5-04214d3dd5b0.dat' input.bam && ln -f -s '/galaxy/server/database/objects/_metadata_files/d/8/d/metadata_d8de2ce9-1135-4da9-8ceb-05ec23272eed.dat' input.bam.bai && sniffles -t ${GALAXY_SLOTS:-2} -m 'input.bam' -v '/galaxy/server/database/objects/8/9/f/dataset_89fe6d7e-3803-4ec9-938a-716c51de47e7.dat' --min_support 10 --max_num_splits 7 --max_distance 1000 --min_length 30 --minmapping_qual 20 --num_reads_report 0 --min_zmw 0 --cluster_support 1 --allelefreq 0.0 --min_homo_af 0.8 --min_het_af 0.3 --skip_parameter_estimation --del_ratio 0.0458369 --ins_ratio 0.049379 --max_diff_per_window 50 --max_dist_aln_events 4", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "parameter_estimation_options": "{\"del_ratio\": \"0.0458369\", \"ins_ratio\": \"0.049379\", \"max_diff_per_window\": \"50\", \"max_dist_aln_events\": \"4\", \"skip_parameter_estimation\": true}", "advanced_options": "{\"ccs_reads\": false, \"ignore_sd\": false, \"not_report_seq\": false, \"report_BND\": false}", "clustering_options": "{\"allelefreq\": \"0.0\", \"cluster\": false, \"cluster_support\": \"1\", \"min_het_af\": \"0.3\", \"min_homo_af\": \"0.8\"}", "general_options": "{\"cs_string\": false, \"max_distance\": \"1000\", \"max_num_splits\": \"7\", \"min_length\": \"30\", \"min_seq_size\": \"\", \"min_support\": \"10\", \"min_zmw\": \"0\", \"minmapping_qual\": \"20\", \"num_reads_report\": \"0\"}"}, "inputs": {"input": {"id": "986140a6d7d4b492", "src": "hda", "uuid": "d485f910-578b-4daf-b4d5-04214d3dd5b0"}}, "outputs": {"output": {"id": "5a0ab83107e1f125", "src": "hda", "uuid": "89fe6d7e-3803-4ec9-938a-716c51de47e7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\tSkip parameter estimation.\nStart parsing... 21\n\tSwitch Chr 21\n\t\tReassessing breakpoints\n\t\tContinue parsing\n\tFinalizing ..\nStart genotype calling:\n\tReopening Bam file for parsing coverage \n\tFinalizing ..\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\tSkip parameter estimation.\nStart parsing... 21\n\tSwitch Chr 21\n\t\tReassessing breakpoints\n\t\tContinue parsing\n\tFinalizing ..\nStart genotype calling:\n\tReopening Bam file for parsing coverage \n\tFinalizing ..\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-11-12 19:22:25", "plugin": "core", "name": "end_epoch", "raw_value": "1731439345.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:22:24", "plugin": "core", "name": "start_epoch", "raw_value": "1731439344.0000000"}, {"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": "vcffixup/1.0.0_rc3+galaxy0-0", "has_data": true, "data": {"tool_id": "vcffixup", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 0, "time_seconds": 33.85781121253967, "inputs": {"input1": {"src": "hda", "id": "1e5b4154869d2527"}}, "job": {"model_class": "Job", "id": "22517353a62337da", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0", "state": "error", "exit_code": null, "create_time": "2024-11-12T19:32:39.003959", "update_time": "2024-11-12T19:32:51.328111", "galaxy_version": "24.1", "external_id": "gxy-rcxxp", "handler": null, "job_runner_name": null, "command_line": "vcffixup '/galaxy/server/database/objects/4/3/8/dataset_4388fc55-f87a-4119-a927-a2b62cec447f.dat' > '/galaxy/server/database/objects/5/0/7/dataset_5074dd1a-a586-4e2b-a282-669b9f6fe7eb.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input1": {"id": "1e5b4154869d2527", "src": "hda", "uuid": "4388fc55-f87a-4119-a927-a2b62cec447f"}}, "outputs": {"out_file1": {"id": "60b15a076fb33d1f", "src": "hda", "uuid": "5074dd1a-a586-4e2b-a282-669b9f6fe7eb"}}, "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/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "vcftools_annotate/0.1-0", "has_data": true, "data": {"tool_id": "vcftools_annotate", "tool_version": "0.1", "test_index": 0, "time_seconds": 40.33533191680908, "inputs": {"input": {"src": "hda", "id": "552969d96b9ac73c"}, "tag": "FORMAT/FREQ", "description": "MinAF [7]", "filter": "MinAF", "condition": ">= 7"}, "job": {"model_class": "Job", "id": "8c9b3cafb9e03de7", "history_id": "aff48f2f86cebb71", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1", "state": "ok", "exit_code": 127, "create_time": "2024-11-12T19:33:13.368469", "update_time": "2024-11-12T19:33:32.626475", "galaxy_version": "24.1", "external_id": "gxy-5bkfv", "handler": null, "job_runner_name": null, "command_line": "echo \"{ tag => 'FORMAT/FREQ', name => 'MinAF', desc => 'MinAF [7]', test => sub { my @t = split('%', @\\$MATCH[0]); return @t[0] >= 7 ? \\$PASS : \\$FAIL }, },\" > f.txt ; vcf-annotate -f f.txt /galaxy/server/database/objects/f/0/d/dataset_f0d69951-a61b-42d0-abb2-632c790eaa4c.dat > /galaxy/server/database/objects/8/1/c/dataset_81cc1242-51b2-4459-9ebb-656fb6e0bd4f.dat", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "condition": "\">= 7\"", "filter": "\"MinAF\"", "description": "\"MinAF [7]\"", "tag": "\"FORMAT/FREQ\""}, "inputs": {"input": {"id": "552969d96b9ac73c", "src": "hda", "uuid": "f0d69951-a61b-42d0-abb2-632c790eaa4c"}}, "outputs": {"output": {"id": "0bdcbf738394aed4", "src": "hda", "uuid": "81cc1242-51b2-4459-9ebb-656fb6e0bd4f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "/galaxy/server/database/jobs_directory/000/209/tool_script.sh: line 22: vcf-annotate: command not found\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "/galaxy/server/database/jobs_directory/000/209/tool_script.sh: line 22: vcf-annotate: command not found\n", "job_messages": [{"code_desc": "tool progress", "desc": "Log: tool progress", "error_level": 1, "match": "/galaxy/server/database/jobs_directory/000/209/tool_script.sh: line 22: vcf-annotate: command not found", "stream": "stderr", "type": "regex"}, {"code_desc": "tool progress", "desc": "Log: tool progress", "error_level": 1, "match": "", "stream": "stdout", "type": "regex"}], "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": "2024-11-12 19:33:19", "plugin": "core", "name": "end_epoch", "raw_value": "1731439999.0000000"}, {"title": "Job Start Time", "value": "2024-11-12 19:33:19", "plugin": "core", "name": "start_epoch", "raw_value": "1731439999.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output output: different than expected, difference (using diff):\n( /tmp/tmpn0q6ym2stest_out1.vcf v. /tmp/tmp9787d7jgtest_out1.vcf )\n--- local_file\n+++ history_data\n@@ -1,30 +0,0 @@\n-##fileformat=VCFv4.1\n-##FILTER=\n-##source_20130813.1=vcf-annotate(r797) -f f.txt \n-#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSample1\n-chr1\t14470\t.\tG\tA\t.\tPASS\tADP=25;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:28:25:23:2:8%:9.8E-1:33:39:22:1:2:0\n-chr1\t14513\t.\tG\tA\t.\tPASS\tADP=32;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:36:32:24:8:25%:9.8E-1:31:22:16:8:7:1\n-chr1\t14626\t.\tG\tC\t.\tPASS\tADP=44;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:45:44:40:4:9.09%:9.8E-1:34:36:14:26:0:4\n-chr1\t14677\t.\tG\tA\t.\tPASS\tADP=70;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:82:70:63:7:10%:9.8E-1:33:17:44:19:7:0\n-chr1\t14813\t.\tT\tG\t.\tMinAF\tADP=105;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:121:105:103:2:1.9%:9.8E-1:32:22:42:61:1:1\n-chr1\t14815\t.\tC\tT\t.\tMinAF\tADP=117;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:122:117:109:8:6.84%:9.8E-1:33:29:50:59:4:4\n-chr1\t14907\t.\tA\tG\t.\tPASS\tADP=104;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:108:104:19:16:45.71%:9.8E-1:37:18:10:9:8:8\n-chr1\t14930\t.\tA\tG\t.\tPASS\tADP=103;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:110:103:17:17:50%:9.8E-1:37:24:8:9:8:9\n-chr1\t15015\t.\tG\tC\t.\tPASS\tADP=52;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:55:52:44:8:15.38%:9.8E-1:34:35:5:39:1:7\n-chr1\t15211\t.\tT\tG\t.\tPASS\tADP=21;WT=0;HET=0;HOM=1;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t1/1:0:23:21:0:2:100%:9.8E-1:0:26:0:0:1:1\n-chr1\t15527\t.\tG\tA\t.\tPASS\tADP=53;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:57:53:29:5:14.71%:9.8E-1:32:23:19:10:3:2\n-chr1\t15688\t.\tC\tT\t.\tPASS\tADP=34;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:36:34:11:4:26.67%:9.8E-1:35:26:6:5:1:3\n-chr1\t16257\t.\tG\tC\t.\tPASS\tADP=23;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:26:23:20:2:9.09%:9.8E-1:35:17:7:13:0:2\n-chr1\t16288\t.\tC\tG\t.\tPASS\tADP=15;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:16:15:11:3:21.43%:9.8E-1:34:36:3:8:1:2\n-chr1\t16298\t.\tC\tT\t.\tPASS\tADP=12;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:12:12:9:2:18.18%:9.8E-1:34:30:2:7:1:1\n-chr1\t16378\t.\tT\tC\t.\tPASS\tADP=24;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:24:24:11:12:52.17%:9.8E-1:37:34:7:4:8:4\n-chr1\t16495\t.\tG\tC\t.\tPASS\tADP=21;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:22:21:14:6:30%:9.8E-1:31:25:5:9:2:4\n-chr1\t16534\t.\tC\tT\t.\tPASS\tADP=11;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:11:11:6:4:40%:9.8E-1:32:37:1:5:0:4\n-chr1\t16571\t.\tG\tA\t.\tPASS\tADP=8;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:8:8:5:2:28.57%:9.8E-1:31:34:2:3:0:2\n-chr1\t16737\t.\tG\tT\t.\tPASS\tADP=27;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:30:27:22:5:18.52%:9.8E-1:37:34:21:1:5:0\n-chr1\t16742\t.\tG\tC\t.\tPASS\tADP=30;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:30:30:23:7:23.33%:9.8E-1:32:37:21:2:7:0\n-chr1\t16900\t.\tT\tC\t.\tMinAF\tADP=140;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:150:140:135:5:3.57%:9.8E-1:35:25:119:16:5:0\n-chr1\t16963\t.\tG\tA\t.\tPASS\tADP=338;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:354:338:297:41:12.13%:9.8E-1:32:34:218:79:26:15\n-chr1\t16977\t.\tG\tA\t.\tPASS\tADP=368;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:384:368:270:98:26.63%:9.8E-1:34:25:186:84:63:35\n-chr1\t16996\t.\tT\tC\t.\tPASS\tADP=356;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:371:356:269:87:24.44%:9.8E-1:35:34:147:122:58:29\n-chr1\t17020\t.\tG\tA\t.\tMinAF\tADP=355;WT=0;HET=1;HOM=0;NC=0\tGT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR\t0/1:0:380:355:347:8:2.25%:9.8E-1:33:29:164:183:4:4\n"], "status": "failure"}}], "galaxy_url": "http://35.185.7.162:8000/galaxy/"} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/results.xunit b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/results.xunit new file mode 100644 index 000000000..1ea719c4e --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/results.xunit @@ -0,0 +1,1128 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] 0.002004 s[racon::Polisher::initialize] aligning overlaps [==> ] 0.002074 s[racon::Polisher::initialize] aligning overlaps [===> ] 0.002159 s[racon::Polisher::initialize] aligning overlaps [====> ] 0.002234 s[racon::Polisher::initialize] aligning overlaps [=====> ] 0.002394 s[racon::Polisher::initialize] aligning overlaps [======> ] 0.002478 s[racon::Polisher::initialize] aligning overlaps [=======> ] 0.002574 s[racon::Polisher::initialize] aligning overlaps [========> ] 0.002673 s[racon::Polisher::initialize] aligning overlaps [=========> ] 0.002785 s[racon::Polisher::initialize] aligning overlaps [==========> ] 0.002868 s[racon::Polisher::initialize] aligning overlaps [===========> ] 0.002986 s[racon::Polisher::initialize] aligning overlaps [============> ] 0.003123 s[racon::Polisher::initialize] aligning overlaps [=============> ] 0.003245 s[racon::Polisher::initialize] aligning overlaps [==============> ] 0.003260 s[racon::Polisher::initialize] aligning overlaps [===============> ] 0.003316 s[racon::Polisher::initialize] aligning overlaps [================> ] 0.003439 s[racon::Polisher::initialize] aligning overlaps [=================> ] 0.003455 s[racon::Polisher::initialize] aligning overlaps [==================> ] 0.003468 s[racon::Polisher::initialize] aligning overlaps [===================>] 0.003582 s[racon::Polisher::initialize] aligning overlaps [====================] 0.003596 s[racon::Polisher::initialize] transformed data into windows 0.000244 s[racon::Polisher::polish] generating consensus [=> ] 0.053768 s[racon::Polisher::polish] generating consensus [==> ] 0.054242 s[racon::Polisher::polish] generating consensus [===> ] 0.086715 s[racon::Polisher::polish] generating consensus [====> ] 0.086876 s[racon::Polisher::polish] generating consensus [=====> ] 0.086894 s[racon::Polisher::polish] generating consensus [======> ] 0.107319 s[racon::Polisher::polish] generating consensus [=======> ] 0.107352 s[racon::Polisher::polish] generating consensus [========> ] 0.110473 s[racon::Polisher::polish] generating consensus [=========> ] 0.162344 s[racon::Polisher::polish] generating consensus [==========> ] 0.169724 s[racon::Polisher::polish] generating consensus [===========> ] 0.253804 s[racon::Polisher::polish] generating consensus [============> ] 0.256505 s[racon::Polisher::polish] generating consensus [=============> ] 0.256539 s[racon::Polisher::polish] generating consensus [==============> ] 0.327457 s[racon::Polisher::polish] generating consensus [===============> ] 0.327752 s[racon::Polisher::polish] generating consensus [================> ] 0.334033 s[racon::Polisher::polish] generating consensus [=================> ] 0.345194 s[racon::Polisher::polish] generating consensus [==================> ] 0.358550 s[racon::Polisher::polish] generating consensus [===================>] 0.413721 s[racon::Polisher::polish] generating consensus [====================] 0.413789 s[racon::Polisher::] total = 0.444241 s + ]]> + + + + + + + + ] 0.013436 s[racon::Polisher::initialize] aligning overlaps [==> ] 0.019887 s[racon::Polisher::initialize] aligning overlaps [===> ] 0.027513 s[racon::Polisher::initialize] aligning overlaps [====> ] 0.030065 s[racon::Polisher::initialize] aligning overlaps [=====> ] 0.035204 s[racon::Polisher::initialize] aligning overlaps [======> ] 0.035404 s[racon::Polisher::initialize] aligning overlaps [=======> ] 0.043280 s[racon::Polisher::initialize] aligning overlaps [========> ] 0.049571 s[racon::Polisher::initialize] aligning overlaps [=========> ] 0.052633 s[racon::Polisher::initialize] aligning overlaps [==========> ] 0.056856 s[racon::Polisher::initialize] aligning overlaps [===========> ] 0.059797 s[racon::Polisher::initialize] aligning overlaps [============> ] 0.064315 s[racon::Polisher::initialize] aligning overlaps [=============> ] 0.074479 s[racon::Polisher::initialize] aligning overlaps [==============> ] 0.077366 s[racon::Polisher::initialize] aligning overlaps [===============> ] 0.091554 s[racon::Polisher::initialize] aligning overlaps [================> ] 0.101872 s[racon::Polisher::initialize] aligning overlaps [=================> ] 0.109477 s[racon::Polisher::initialize] aligning overlaps [==================> ] 0.110131 s[racon::Polisher::initialize] aligning overlaps [===================>] 0.110152 s[racon::Polisher::initialize] aligning overlaps [====================] 0.113696 s[racon::Polisher::initialize] transformed data into windows 0.000346 s[racon::Polisher::polish] generating consensus [=> ] 0.020773 s[racon::Polisher::polish] generating consensus [==> ] 0.021827 s[racon::Polisher::polish] generating consensus [===> ] 0.040910 s[racon::Polisher::polish] generating consensus [====> ] 0.041045 s[racon::Polisher::polish] generating consensus [=====> ] 0.051303 s[racon::Polisher::polish] generating consensus [======> ] 0.051497 s[racon::Polisher::polish] generating consensus [=======> ] 0.058868 s[racon::Polisher::polish] generating consensus [========> ] 0.058934 s[racon::Polisher::polish] generating consensus [=========> ] 0.068434 s[racon::Polisher::polish] generating consensus [==========> ] 0.068462 s[racon::Polisher::polish] generating consensus [===========> ] 0.086587 s[racon::Polisher::polish] generating consensus [============> ] 0.086614 s[racon::Polisher::polish] generating consensus [=============> ] 0.118306 s[racon::Polisher::polish] generating consensus [==============> ] 0.120215 s[racon::Polisher::polish] generating consensus [===============> ] 0.148133 s[racon::Polisher::polish] generating consensus [================> ] 0.160936 s[racon::Polisher::polish] generating consensus [=================> ] 0.173231 s[racon::Polisher::polish] generating consensus [==================> ] 0.173879 s[racon::Polisher::polish] generating consensus [===================>] 0.189225 s[racon::Polisher::polish] generating consensus [====================] 0.237113 s[racon::Polisher::] total = 0.365879 s + ]]> + + + + + + + + ] 0.002207 s[racon::Polisher::initialize] aligning overlaps [==> ] 0.002319 s[racon::Polisher::initialize] aligning overlaps [===> ] 0.002487 s[racon::Polisher::initialize] aligning overlaps [====> ] 0.002623 s[racon::Polisher::initialize] aligning overlaps [=====> ] 0.002689 s[racon::Polisher::initialize] aligning overlaps [======> ] 0.002762 s[racon::Polisher::initialize] aligning overlaps [=======> ] 0.002919 s[racon::Polisher::initialize] aligning overlaps [========> ] 0.003217 s[racon::Polisher::initialize] aligning overlaps [=========> ] 0.003304 s[racon::Polisher::initialize] aligning overlaps [==========> ] 0.003320 s[racon::Polisher::initialize] aligning overlaps [===========> ] 0.003426 s[racon::Polisher::initialize] aligning overlaps [============> ] 0.003551 s[racon::Polisher::initialize] aligning overlaps [=============> ] 0.003565 s[racon::Polisher::initialize] aligning overlaps [==============> ] 0.003666 s[racon::Polisher::initialize] aligning overlaps [===============> ] 0.003682 s[racon::Polisher::initialize] aligning overlaps [================> ] 0.003693 s[racon::Polisher::initialize] aligning overlaps [=================> ] 0.003705 s[racon::Polisher::initialize] aligning overlaps [==================> ] 0.003720 s[racon::Polisher::initialize] aligning overlaps [===================>] 0.003767 s[racon::Polisher::initialize] aligning overlaps [====================] 0.003782 s[racon::Polisher::initialize] transformed data into windows 0.000361 s[racon::Polisher::polish] generating consensus [=> ] 0.029112 s[racon::Polisher::polish] generating consensus [==> ] 0.032169 s[racon::Polisher::polish] generating consensus [===> ] 0.055828 s[racon::Polisher::polish] generating consensus [====> ] 0.055888 s[racon::Polisher::polish] generating consensus [=====> ] 0.066559 s[racon::Polisher::polish] generating consensus [======> ] 0.066617 s[racon::Polisher::polish] generating consensus [=======> ] 0.076605 s[racon::Polisher::polish] generating consensus [========> ] 0.076695 s[racon::Polisher::polish] generating consensus [=========> ] 0.087819 s[racon::Polisher::polish] generating consensus [==========> ] 0.090359 s[racon::Polisher::polish] generating consensus [===========> ] 0.108593 s[racon::Polisher::polish] generating consensus [============> ] 0.114878 s[racon::Polisher::polish] generating consensus [=============> ] 0.142685 s[racon::Polisher::polish] generating consensus [==============> ] 0.151782 s[racon::Polisher::polish] generating consensus [===============> ] 0.175327 s[racon::Polisher::polish] generating consensus [================> ] 0.180405 s[racon::Polisher::polish] generating consensus [=================> ] 0.201931 s[racon::Polisher::polish] generating consensus [==================> ] 0.201981 s[racon::Polisher::polish] generating consensus [===================>] 0.218374 s[racon::Polisher::polish] generating consensus [====================] 0.251099 s[racon::Polisher::] total = 0.281345 s + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/tools.yml b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/tools.yml new file mode 100644 index 000000000..96c903b6a --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/tools.yml @@ -0,0 +1,127 @@ +chunk: 3 +tools: +- name: racon + owner: bgruening + revisions: + - a199cd7ac344 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: deeptools_compute_gc_bias + owner: bgruening + revisions: + - 2bc10a9ca58b + tool_panel_section_id: deeptools + tool_panel_section_label: deepTools +- name: fastq_manipulation + owner: devteam + revisions: + - 5b87038565bb + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: ncbi_acc_download + owner: iuc + revisions: + - 1c58de56d587 + tool_panel_section_id: get_data + tool_panel_section_label: Get Data +- name: mummer_show_coords + owner: iuc + revisions: + - 959c1f8dae95 + tool_panel_section_id: multiple_alignments + tool_panel_section_label: Multiple Alignments +- name: poretools_squiggle + owner: iuc + revisions: + - 34553d0caa5e + tool_panel_section_id: nanopore + tool_panel_section_label: Nanopore +- name: kallisto_quant + owner: iuc + revisions: + - 60f888039fb2 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: bamtools + owner: devteam + revisions: + - 4d343c1f606b + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: samtools_idxstats + owner: devteam + revisions: + - 7a6034296ae9 + - 7def34e6cf4d + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: music_inspect_eset + owner: bgruening + revisions: + - 2fed32b5aa02 + - 7705cc75ac18 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: raceid_inspectclusters + owner: iuc + revisions: + - 2b0d3e2f402a + - 41f34e925bd5 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scater_plot_pca + owner: iuc + revisions: + - 46fc6751d746 + - c99ba278dfa9 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_filter_cells + owner: ebi-gxa + revisions: + - 4c42e5d8cb7c + - ba64b91ed2b9 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: column_maker + owner: devteam + revisions: + - 02026300aa45 + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: column_order_header_sort + owner: iuc + revisions: + - 6ae9724caf4d + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: sniffles + owner: iuc + revisions: + - 93c4b04a0769 + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: bcftools_concat + owner: iuc + revisions: + - d40d4bf05718 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: bcftools_annotate + owner: iuc + revisions: + - 403553ae19f6 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: 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