diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md index aa97cc2ce..5f5936dc5 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 Oct 23 06:24:58 2023Mon Oct 16 06:23:58 2023
1ToolsetMon Oct 23 18:26:34 2023Mon Oct 16 18:29:10 2023
2ToolsetTue Oct 24 06:23:29 2023Tue Oct 17 06:22:52 2023
3ToolsetTue Oct 17 18:30:41 2023Tue Oct 10 18:28:40 2023
4ToolsetWed Oct 18 06:24:04 2023Wed Oct 11 06:23:00 2023
5ToolsetWed Oct 18 18:29:46 2023Wed Oct 11 18:30:44 2023
6ToolsetThu Oct 19 06:23:54 2023Thu Oct 12 06:25:28 2023
7ToolsetThu Oct 19 18:31:15 2023Thu Sep 28 18:27:22 2023
8ToolsetFri Oct 20 06:23:01 2023Fri Oct 13 06:23:52 2023
9ToolsetFri Oct 20 18:29:34 2023Fri Oct 13 18:28:37 2023
10ToolsetSat Oct 21 06:21:06 2023Sat Oct 14 06:24:13 2023
11ToolsetSat Oct 21 18:28:12 2023Sat Oct 14 18:29:05 2023
12ToolsetSun Oct 22 06:21:10 2023Sun Oct 15 06:23:21 2023
13ToolsetSun Oct 22 18:27:29 2023Sun Oct 15 18:29:44 2023
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Oct 23 06:24:58 2023Mon Oct 16 06:23:58 2023
1ToolsetMon Oct 23 18:26:34 2023Mon Oct 16 18:29:10 2023
2ToolsetTue Oct 24 06:23:29 2023Tue Oct 17 06:22:52 2023
3ToolsetTue Oct 24 18:30:54 2023Tue Oct 17 18:30:41 2023
4ToolsetWed Oct 18 06:24:04 2023Wed Oct 11 06:23:00 2023
5ToolsetWed Oct 18 18:29:46 2023Wed Oct 11 18:30:44 2023
6ToolsetThu Oct 19 06:23:54 2023Thu Oct 12 06:25:28 2023
7ToolsetThu Oct 19 18:31:15 2023Thu Sep 28 18:27:22 2023
8ToolsetFri Oct 20 06:23:01 2023Fri Oct 13 06:23:52 2023
9ToolsetFri Oct 20 18:29:34 2023Fri Oct 13 18:28:37 2023
10ToolsetSat Oct 21 06:21:06 2023Sat Oct 14 06:24:13 2023
11ToolsetSat Oct 21 18:28:12 2023Sat Oct 14 18:29:05 2023
12ToolsetSun Oct 22 06:21:10 2023Sun Oct 15 06:23:21 2023
13ToolsetSun Oct 22 18:27:29 2023Sun Oct 15 18:29:44 2023
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json index c6b2ba96f..926743c4d 100644 --- a/reports/anvil-edge/tool-tests/chunks.json +++ b/reports/anvil-edge/tool-tests/chunks.json @@ -14,11 +14,11 @@ "date2": "Tue Oct 17 06:22:52 2023" }, "3": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-17-18-13-1/results.html", - "date1": "Tue Oct 17 18:30:41 2023", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-17-18-13-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-10-18-13-1/results.html", - "date2": "Tue Oct 10 18:28:40 2023" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/results.html", + "date1": "Tue Oct 24 18:30:54 2023", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-17-18-13-1/results.html", + "date2": "Tue Oct 17 18:30:41 2023" }, "4": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-18-06-08-1/results.html", diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/chunk.json b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/chunk.json new file mode 100644 index 000000000..04a33e21f --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/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-23-10-24-18-13-1/results.html", + "date1": "Tue Oct 24 18:30:54 2023", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/chunk.txt new file mode 100644 index 000000000..d0d4a0789 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/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-23-10-24-18-13-1/errors/11f10f91ff4f160b.json b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/errors/11f10f91ff4f160b.json new file mode 100644 index 000000000..51629d4e1 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/errors/11f10f91ff4f160b.json @@ -0,0 +1,97 @@ +{ + "model_class": "Job", + "id": "11f10f91ff4f160b", + "state": "error", + "exit_code": 1, + "update_time": "2023-10-24T18:47:22.553600", + "create_time": "2023-10-24T18:47:06.070631", + "galaxy_version": "23.1", + "command_version": "", + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0", + "history_id": "ac0b688889bc6865", + "external_id": "gxy-fzxjc", + "command_line": "echo 'CP011064,CP0XXXXX,CP021680' | sed -r 's/(\\,|__cn__)/\\n/g' | grep -v \"^[ \\t]*$\" > accessions && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'fasta' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", + "traceback": null, + "params": { + "__input_ext": "\"data\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "ignore_failed": "\"0\"", + "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": "799d0bfb7f1bdb54", + "src": "hda", + "uuid": "d1c94233-5843-4d39-a5a8-6f74648f9e7c" + }, + "__new_primary_file_output|CP011064__": { + "id": "5b2f017fabdab700", + "src": "hda", + "uuid": "43f58e33-fab1-49ac-a8e6-09d650c448ba" + } + }, + "output_collections": { + "output": { + "id": "b9bef7d910419ef5", + "src": "hdca" + } + }, + "tool_stdout": "", + "tool_stderr": "Failed to download file with id CP0XXXXX from NCBI\nTraceback (most recent call last):\n File \"/usr/local/bin/ncbi-acc-download\", line 10, in \n sys.exit(main())\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/__main__.py\", line 54, in main\n download_to_file(dl_id, config, filename, append)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/core.py\", line 110, in download_to_file\n r = get_stream(url, params)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/download.py\", line 90, in get_stream\n raise DownloadError(\"Download failed with return code: {}\".format(r.status_code))\nncbi_acc_download.errors.DownloadError: Download failed with return code: 400\n", + "job_stdout": "", + "job_stderr": "", + "stderr": "Failed to download file with id CP0XXXXX from NCBI\nTraceback (most recent call last):\n File \"/usr/local/bin/ncbi-acc-download\", line 10, in \n sys.exit(main())\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/__main__.py\", line 54, in main\n download_to_file(dl_id, config, filename, append)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/core.py\", line 110, in download_to_file\n r = get_stream(url, params)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/download.py\", line 90, in get_stream\n raise DownloadError(\"Download failed with return code: {}\".format(r.status_code))\nncbi_acc_download.errors.DownloadError: Download failed with return code: 400\n", + "stdout": "", + "job_messages": [ + { + "code_desc": "", + "desc": "Fatal error: Exit code 1 ()", + "error_level": 3, + "exit_code": 1, + "type": "exit_code" + } + ], + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [ + { + "title": "Job Runtime (Wall Clock)", + "value": "3 seconds", + "plugin": "core", + "name": "runtime_seconds", + "raw_value": "3.0000000" + }, + { + "title": "Job End Time", + "value": "2023-10-24 18:47:11", + "plugin": "core", + "name": "end_epoch", + "raw_value": "1698173231.0000000" + }, + { + "title": "Job Start Time", + "value": "2023-10-24 18:47:08", + "plugin": "core", + "name": "start_epoch", + "raw_value": "1698173228.0000000" + }, + { + "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-23-10-24-18-13-1/errors/1486d3c4f6725a5b.json b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/errors/1486d3c4f6725a5b.json new file mode 100644 index 000000000..19e3582c8 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/errors/1486d3c4f6725a5b.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "1486d3c4f6725a5b", + "state": "error", + "exit_code": null, + "update_time": "2023-10-24T18:53:35.706032", + "create_time": "2023-10-24T18:53:24.154809", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "ac0b688889bc6865", + "external_id": "gxy-l7l4s", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/77/registry.xml' '/galaxy/server/database/jobs_directory/000/77/upload_params.json' '107:/galaxy/server/database/objects/4/5/0/dataset_4504cc8b-b39e-4ad6-ba82-2eeaad435b1e_files:/galaxy/server/database/objects/4/5/0/dataset_4504cc8b-b39e-4ad6-ba82-2eeaad435b1e.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_3v9luuae\"", + "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"felCat8_chrM.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_9hjsh3fu\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fasta\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "d3e8c30c887d1fc7", + "src": "hda", + "uuid": "4504cc8b-b39e-4ad6-ba82-2eeaad435b1e" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/errors/2690ce60900b8d77.json b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/errors/2690ce60900b8d77.json new file mode 100644 index 000000000..dde3d57ff --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/errors/2690ce60900b8d77.json @@ -0,0 +1,44 @@ +{ + "model_class": "Job", + "id": "2690ce60900b8d77", + "state": "error", + "exit_code": null, + "update_time": "2023-10-24T19:24:04.441693", + "create_time": "2023-10-24T19:23:53.497876", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "upload1", + "history_id": "ac0b688889bc6865", + "external_id": "gxy-w6njw", + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/192/registry.xml' '/galaxy/server/database/jobs_directory/000/192/upload_params.json' '236:/galaxy/server/database/objects/c/1/8/dataset_c18af32b-a766-400a-813e-a0ad98d99cfe_files:/galaxy/server/database/objects/c/1/8/dataset_c18af32b-a766-400a-813e-a0ad98d99cfe.dat'", + "traceback": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_begkxmpz\"", + "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"test_in1.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_j87c0pbv\", \"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": "011140a76a787afb", + "src": "hda", + "uuid": "c18af32b-a766-400a-813e-a0ad98d99cfe" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/errors/33095ef16140ba3b.json b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/errors/33095ef16140ba3b.json new file mode 100644 index 000000000..1845d0438 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/errors/33095ef16140ba3b.json @@ -0,0 +1,55 @@ +{ + "model_class": "Job", + "id": "33095ef16140ba3b", + "state": "error", + "exit_code": null, + "update_time": "2023-10-24T19:09:37.249706", + "create_time": "2023-10-24T19:09:26.576999", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy2", + "history_id": "ac0b688889bc6865", + "external_id": "gxy-qwhdv", + "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/2b0d3e2f402a/raceid_inspectclusters/scripts/clusterinspect.R' '/galaxy/server/database/jobs_directory/000/133/configs/tmp4khvbq8s' &> '/galaxy/server/database/objects/a/8/f/dataset_a8f48fd2-533f-473f-82ec-9f4456d0ed85.dat'", + "traceback": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "diffgtest": "{\"__current_case__\": 1, \"do_opt\": \"yes\", \"set_a\": {\"meth\": {\"__current_case__\": 1, \"selector\": \"^V5.*\", \"type\": \"regex\"}, \"name_set\": \"Test set A\"}, \"set_b\": {\"meth\": {\"__current_case__\": 2, \"selector\": \"I5d_3,I5d_4,I5d_6,I5d_8,I5d_9,I5d_10,I5d_11,I5d_12,I5d_13,I5d_14\", \"type\": \"manual\"}, \"name_set\": \"Test set B\"}, \"use\": {\"__current_case__\": 1, \"def\": \"no\", \"plotdiffg_lthr\": \"0.2\", \"plotdiffg_mthr\": \"0.2\", \"plotdiffg_padj\": false, \"plotdiffg_pthr\": \"0.1\", \"plotdiffg_show_names\": true}}", + "gois": "{\"__current_case__\": 1, \"do_opt\": \"yes\", \"inspect_goi_cells\": null, \"inspect_goi_genes\": \"Apoa1,Apoa1bp,Apoa2,Apoa4,Apoa5\", \"use\": {\"__current_case__\": 1, \"def\": \"no\", \"inspect_goi_imputed\": false, \"plotexp_n\": \"Test Title\", \"plotmarkg_aggr\": true, \"plotmarkg_cap\": \"100\", \"plotmarkg_cl\": null, \"plotmarkg_cluster_cols\": true, \"plotmarkg_cluster_rows\": false, \"plotmarkg_cluster_set\": true, \"plotmarkg_cthr\": \"0\", \"plotmarkg_flo\": \"-10\", \"plotmarkg_norm\": true, \"plotmarkg_order_cells\": true, \"plotmarkg_samples\": \"(\\\\\\\\_\\\\\\\\d+)$\"}}", + "plotsym": "{\"__current_case__\": 1, \"do_opt\": \"yes\", \"types_regex\": \"\\\\\\\\_\\\\\\\\d+\", \"use\": {\"__current_case__\": 1, \"def\": \"no\", \"fr\": true, \"subset_regex\": \"IV|V\"}}", + "plotgen": "{\"__current_case__\": 1, \"clusts_plot\": \"\", \"do_opt\": \"yes\"}" + }, + "inputs": { + "inputrds": { + "id": "2e89c0b970036ba9", + "src": "hda", + "uuid": "842c1525-6ebf-4559-bd46-16caed4a95f8" + } + }, + "outputs": { + "outpdf": { + "id": "e9d99367ce35acfe", + "src": "hda", + "uuid": "dcba375e-59ac-4849-ab60-ff553839c112" + }, + "outlog": { + "id": "86714f837e34f213", + "src": "hda", + "uuid": "a8f48fd2-533f-473f-82ec-9f4456d0ed85" + } + }, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stderr": "", + "stdout": "", + "job_messages": null, + "dependencies": [], + "user_email": "tests@fake.org", + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/errors/3bcef82d73bbd8f0.json b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/errors/3bcef82d73bbd8f0.json new file mode 100644 index 000000000..075e2ebdd --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/errors/3bcef82d73bbd8f0.json @@ -0,0 +1,48 @@ +{ + "model_class": "Job", + "id": "3bcef82d73bbd8f0", + "state": "error", + "exit_code": null, + "update_time": "2023-10-24T18:40:04.723226", + "create_time": "2023-10-24T18:39:59.226366", + "galaxy_version": "23.1", + "command_version": null, + "copied_from_job_id": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5", + "history_id": "ac0b688889bc6865", + "external_id": "gxy-hdkkh", + "command_line": "gx-fastq-manipulation '/galaxy/server/database/objects/6/f/7/dataset_6f7cba4d-121a-4107-ac9e-567a1482f275.dat' '/galaxy/server/database/jobs_directory/000/29/configs/tmpgriatoc9' '/galaxy/server/database/objects/2/5/8/dataset_258c91ee-c266-47ab-a31f-d4aa013296ac.dat' '/galaxy/server/database/objects/2/5/8/dataset_258c91ee-c266-47ab-a31f-d4aa013296ac_files' 'sanger'", + "traceback": null, + "params": { + "__input_ext": "\"fastqsanger\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "manipulate_blocks": "[{\"__index__\": 0, \"manipulation_type\": {\"__current_case__\": 1, \"manipulation\": {\"__current_case__\": 0, \"manipulation_selector\": \"rev_comp\"}, 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+
+ + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/results.json b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/results.json new file mode 100644 index 000000000..87133e3ba --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 89, "errors": 8, "failures": 5, "skips": 0}, "tests": [{"id": "bamtools/2.4.0.0-0", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.4.0.0", "test_index": 0, "time_seconds": 40.92435145378113, "inputs": {"input_bams": {"src": "hda", "id": "490837d49529ccb4"}, "analysis_type|format_type|reference_source|ref_file": {"src": "hda", "id": "c2e201b408e2756c"}, "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": "058d1fe990cd4e62", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:55:17.575578", "create_time": "2023-10-24T18:54:59.084865", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0", "history_id": "ac0b688889bc6865", "external_id": "gxy-4zrvz", "command_line": "ln -s '/galaxy/server/database/objects/7/f/b/dataset_7fbcab0e-1e43-44de-b44c-6b13d5610133.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/4/a/8/metadata_4a8fbb8f-bb81-47e8-8ccf-ed461922a981.dat' localbam.bam.bai && ln -s '/galaxy/server/database/objects/9/c/4/dataset_9c4e1227-66f8-4558-ba19-d91a417da927.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/e/7/4/dataset_e741a703-e920-4657-9b1c-0a57283c63dc.dat' -in localbam.bam", "traceback": null, "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\": 119, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}}}"}, "inputs": {"input_bams": {"id": "490837d49529ccb4", "src": "hda", "uuid": "7fbcab0e-1e43-44de-b44c-6b13d5610133"}, "analysis_type|format_type|reference_source|ref_file": {"id": "c2e201b408e2756c", "src": "hda", "uuid": "9c4e1227-66f8-4558-ba19-d91a417da927"}}, "outputs": {"out_file1": {"id": "4cdebb87277eb5de", "src": "hda", "uuid": "e741a703-e920-4657-9b1c-0a57283c63dc"}}, "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": "", "stderr": "Pileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 18:55:06", "plugin": "core", "name": "end_epoch", "raw_value": "1698173706.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:55:06", "plugin": "core", "name": "start_epoch", "raw_value": "1698173706.0000000"}, {"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/2.4.0.0-1", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.4.0.0", "test_index": 1, "time_seconds": 30.763237476348877, "inputs": {"input_bams": {"src": "hda", "id": "f87cac36120888be"}, "analysis_type|analysis_type_selector": "count"}, "job": {"model_class": "Job", "id": "dd911df7ab19efb9", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:55:48.863730", "create_time": "2023-10-24T18:55:37.284434", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0", "history_id": "ac0b688889bc6865", "external_id": "gxy-52v7c", "command_line": "ln -s '/galaxy/server/database/objects/5/7/4/dataset_574dd857-01a1-427a-a332-e44ef8a4b7c2.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/0/1/1/metadata_0116e098-2d24-4933-ad19-f935b70c61bd.dat' localbam.bam.bai && bamtools count > '/galaxy/server/database/objects/4/e/2/dataset_4e221e75-4a76-4693-aabf-790be36c2d9f.dat' -in localbam.bam", "traceback": null, "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": "f87cac36120888be", "src": "hda", "uuid": "574dd857-01a1-427a-a332-e44ef8a4b7c2"}}, "outputs": {"out_file1": {"id": "7e7aed4494bd14ef", "src": "hda", "uuid": "4e221e75-4a76-4693-aabf-790be36c2d9f"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 18:55:38", "plugin": "core", "name": "end_epoch", "raw_value": "1698173738.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:55:38", "plugin": "core", "name": "start_epoch", "raw_value": "1698173738.0000000"}, {"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/2.4.0.0-2", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.4.0.0", "test_index": 2, "time_seconds": 32.46080565452576, "inputs": {"input_bams": {"src": "hda", "id": "0c6b68883575c7e5"}, "analysis_type|analysis_type_selector": "coverage"}, "job": {"model_class": "Job", "id": "c86ea752d7a23f3a", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:56:21.278278", "create_time": "2023-10-24T18:56:08.557249", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0.0", "history_id": "ac0b688889bc6865", "external_id": "gxy-grh4b", "command_line": "ln -s '/galaxy/server/database/objects/c/7/9/dataset_c79130e4-51bd-47e8-babe-c90a66513a71.dat' localbam.bam && ln -s '/galaxy/server/database/objects/_metadata_files/9/d/a/metadata_9dab5fc4-4595-482f-a365-6adebc23f77d.dat' localbam.bam.bai && bamtools coverage -out '/galaxy/server/database/objects/8/6/d/dataset_86d62fa3-b84a-4855-b0d2-a36c98127b5d.dat' -in localbam.bam", "traceback": null, "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": "0c6b68883575c7e5", "src": "hda", "uuid": "c79130e4-51bd-47e8-babe-c90a66513a71"}}, "outputs": {"out_file1": {"id": "dd7fb4a19ae724cb", "src": "hda", "uuid": "86d62fa3-b84a-4855-b0d2-a36c98127b5d"}}, "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": "", "stderr": "Pileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\nPileup::Run() : Data not sorted correctly!\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 18:56:10", "plugin": "core", "name": "end_epoch", "raw_value": "1698173770.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:56:10", "plugin": "core", "name": "start_epoch", "raw_value": "1698173770.0000000"}, {"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/2.4.0.0-3", "has_data": true, "data": {"tool_id": "bamtools", "tool_version": "2.4.0.0", "test_index": 3, "time_seconds": 12.21846055984497, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_annotate/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.10", "test_index": 0, "time_seconds": 38.27225184440613, "inputs": {"input_file": {"src": "hda", "id": "2c928ec99e9db6aa"}, "sec_annofile|columns": "CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL", "sec_annofile|annofile|annotations": {"src": "hda", "id": "9fd4eb726f107959"}, "sec_annofile|annofile|header_file": {"src": "hda", "id": "e73ff3ecc285a613"}, "sec_annofile|annofile|anno_fmt": "tab", "output_type": "v"}, "job": {"model_class": "Job", "id": "1dbf7ee80d01d527", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:19:12.029349", "create_time": "2023-10-24T19:18:59.228969", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10", "history_id": "ac0b688889bc6865", "external_id": "gxy-fmmdf", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/d/0/b/dataset_d0badb83-e0d9-4bb8-ac73-89d4f8df071f.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c \"/galaxy/server/database/objects/6/d/3/dataset_6d31323f-93c4-42e2-98cf-606eb62bfaa3.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/5/c/5/dataset_5c5e316a-fc7c-4a59-9e94-a3e63e27d64e.dat\" --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/9/d/2/dataset_9d214ce2-0432-4b61-bd1f-2a7d7e60a220.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "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__\"}, \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"\", \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 2, \"anno_fmt\": \"tab\", \"annotations\": {\"values\": [{\"id\": 211, \"src\": \"hda\"}]}, \"header_file\": {\"values\": [{\"id\": 212, \"src\": \"hda\"}]}, \"header_lines\": null}, \"columns\": \"CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL\", \"mark_sites\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "2c928ec99e9db6aa", "src": "hda", "uuid": "d0badb83-e0d9-4bb8-ac73-89d4f8df071f"}, "sec_annofile|annofile|annotations": {"id": "9fd4eb726f107959", "src": "hda", "uuid": "6d31323f-93c4-42e2-98cf-606eb62bfaa3"}, "sec_annofile|annofile|header_file": {"id": "e73ff3ecc285a613", "src": "hda", "uuid": "5c5e316a-fc7c-4a59-9e94-a3e63e27d64e"}}, "outputs": {"output_file": {"id": "0f6fafacce319d56", "src": "hda", "uuid": "9d214ce2-0432-4b61-bd1f-2a7d7e60a220"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 19:19:01", "plugin": "core", "name": "end_epoch", "raw_value": "1698175141.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:19:01", "plugin": "core", "name": "start_epoch", "raw_value": "1698175141.0000000"}, {"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/1.10-1", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.10", "test_index": 1, "time_seconds": 37.98457980155945, "inputs": {"input_file": {"src": "hda", "id": "46d5012f314d0940"}, "sec_annofile|columns": "CHROM,FROM,TO,T_STR", "sec_annofile|annofile|annotations": {"src": "hda", "id": "30055c989b7639e0"}, "sec_annofile|annofile|header_file": {"src": "hda", "id": "904254e366199ea4"}, "sec_annofile|annofile|anno_fmt": "tab", "output_type": "v"}, "job": {"model_class": "Job", "id": "2e89c0b970036ba9", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:19:50.334563", "create_time": "2023-10-24T19:19:36.985868", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10", "history_id": "ac0b688889bc6865", "external_id": "gxy-lq5cl", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/a/2/dataset_fa29b142-6f30-4ece-aaff-f2b4598a0abc.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c \"/galaxy/server/database/objects/2/9/f/dataset_29f11d2d-dce5-48ef-a2aa-a0cd63073d39.dat\" > annotations.bed.gz && tabix -s 1 -b 2 -e 3 annotations.bed.gz && bcftools annotate --columns 'CHROM,FROM,TO,T_STR' --annotations \"annotations.bed.gz\" --header-lines \"/galaxy/server/database/objects/b/a/7/dataset_ba739458-aa59-4569-93f3-96ba3919809e.dat\" --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/8/7/1/dataset_871f659d-e509-4052-81c2-034d6b85369b.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "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__\"}, \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"\", \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 2, \"anno_fmt\": \"tab\", \"annotations\": {\"values\": [{\"id\": 215, \"src\": \"hda\"}]}, \"header_file\": {\"values\": [{\"id\": 216, \"src\": \"hda\"}]}, \"header_lines\": null}, \"columns\": \"CHROM,FROM,TO,T_STR\", \"mark_sites\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "46d5012f314d0940", "src": "hda", "uuid": "fa29b142-6f30-4ece-aaff-f2b4598a0abc"}, "sec_annofile|annofile|annotations": {"id": "30055c989b7639e0", "src": "hda", "uuid": "29f11d2d-dce5-48ef-a2aa-a0cd63073d39"}, "sec_annofile|annofile|header_file": {"id": "904254e366199ea4", "src": "hda", "uuid": "ba739458-aa59-4569-93f3-96ba3919809e"}}, "outputs": {"output_file": {"id": "81333d616be07d4c", "src": "hda", "uuid": "871f659d-e509-4052-81c2-034d6b85369b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 19:19:39", "plugin": "core", "name": "end_epoch", "raw_value": "1698175179.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:19:39", "plugin": "core", "name": "start_epoch", "raw_value": "1698175179.0000000"}, {"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/1.10-2", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.10", "test_index": 2, "time_seconds": 32.70191192626953, "inputs": {"input_file": {"src": "hda", "id": "01a1ab151a2af9d7"}, "sec_annofile|columns": "STR,ID,QUAL,FILTER", "sec_annofile|annofile|annotations": {"src": "hda", "id": "06e4b5d8b468fc88"}, "sec_annofile|annofile|anno_fmt": "vcf", "output_type": "v"}, "job": {"model_class": "Job", "id": "79fa2fa07ac6333d", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:20:23.069808", "create_time": "2023-10-24T19:20:10.660784", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10", "history_id": "ac0b688889bc6865", "external_id": "gxy-x6g7g", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/6/a/dataset_86a7d22d-c77c-48d8-8c4c-4ffb377df73b.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c \"/galaxy/server/database/objects/b/e/4/dataset_be416741-5197-4379-a0f5-21a7ebb9468f.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/7/c/5/dataset_7c56e698-49c7-46c6-b5c3-b5b711e49d6b.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "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__\"}, \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"\", \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 1, \"anno_fmt\": \"vcf\", \"annotations\": {\"values\": [{\"id\": 219, \"src\": \"hda\"}]}}, \"columns\": \"STR,ID,QUAL,FILTER\", \"mark_sites\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "01a1ab151a2af9d7", "src": "hda", "uuid": "86a7d22d-c77c-48d8-8c4c-4ffb377df73b"}, "sec_annofile|annofile|annotations": {"id": "06e4b5d8b468fc88", "src": "hda", "uuid": "be416741-5197-4379-a0f5-21a7ebb9468f"}}, "outputs": {"output_file": {"id": "9050dd791385b9fd", "src": "hda", "uuid": "7c56e698-49c7-46c6-b5c3-b5b711e49d6b"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-24 19:20:13", "plugin": "core", "name": "end_epoch", "raw_value": "1698175213.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:20:12", "plugin": "core", "name": "start_epoch", "raw_value": "1698175212.0000000"}, {"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/1.10-3", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.10", "test_index": 3, "time_seconds": 34.43739628791809, "inputs": {"input_file": {"src": "hda", "id": "5214f5829c94c324"}, "sec_annofile|columns": "STR,ID,QUAL,FILTER", "sec_annofile|annofile|annotations": {"src": "hda", "id": "ac30c2a830e49e37"}, "sec_annofile|annofile|anno_fmt": "vcf", "output_type": "v"}, "job": {"model_class": "Job", "id": "c618c8b87838dbd1", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:20:57.730039", "create_time": "2023-10-24T19:20:44.388685", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10", "history_id": "ac0b688889bc6865", "external_id": "gxy-58rbd", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/4/5/1/dataset_4515594c-8433-49b4-845f-c70ccb9571c5.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/7/b/f/dataset_7bf0629c-78c6-462c-9cc8-d95f49f0a5f3.dat' annotations.bcf && ln -s '/galaxy/server/database/objects/_metadata_files/e/2/5/metadata_e25415d8-33d8-413d-a0ea-17270987804f.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/d/f/6/dataset_df639fa7-e030-463b-aa4a-7a11f9322e96.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "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__\"}, \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"\", \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 1, \"anno_fmt\": \"vcf\", \"annotations\": {\"values\": [{\"id\": 222, \"src\": \"hda\"}]}}, \"columns\": \"STR,ID,QUAL,FILTER\", \"mark_sites\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "5214f5829c94c324", "src": "hda", "uuid": "4515594c-8433-49b4-845f-c70ccb9571c5"}, "sec_annofile|annofile|annotations": {"id": "ac30c2a830e49e37", "src": "hda", "uuid": "7bf0629c-78c6-462c-9cc8-d95f49f0a5f3"}}, "outputs": {"output_file": {"id": "2f2ccf6b89810d3b", "src": "hda", "uuid": "df639fa7-e030-463b-aa4a-7a11f9322e96"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-24 19:20:47", "plugin": "core", "name": "end_epoch", "raw_value": "1698175247.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:20:46", "plugin": "core", "name": "start_epoch", "raw_value": "1698175246.0000000"}, {"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/1.10-4", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.10", "test_index": 4, "time_seconds": 33.511348247528076, "inputs": {"input_file": {"src": "hda", "id": "884980805663e3ef"}, "sec_annofile|columns": "ID,QUAL,FILTER,INFO,FMT", "sec_annofile|annofile|annotations": {"src": "hda", "id": "49223a3fae466eab"}, "sec_annofile|annofile|anno_fmt": "vcf", "output_type": "v"}, "job": {"model_class": "Job", "id": "590b886f66f35276", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:21:31.272920", "create_time": "2023-10-24T19:21:18.499195", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10", "history_id": "ac0b688889bc6865", "external_id": "gxy-pw9jg", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/e/2/3/dataset_e230c6bc-f2bb-4dab-99d0-18a1cc3a8e99.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c \"/galaxy/server/database/objects/7/3/7/dataset_7377a1eb-ee36-46a9-94b3-2a22648721cf.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/0/b/4/dataset_0b499c54-a360-42f1-856c-9d8e056c26d9.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "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__\"}, \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"\", \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 1, \"anno_fmt\": \"vcf\", \"annotations\": {\"values\": [{\"id\": 225, \"src\": \"hda\"}]}}, \"columns\": \"ID,QUAL,FILTER,INFO,FMT\", \"mark_sites\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "884980805663e3ef", "src": "hda", "uuid": "e230c6bc-f2bb-4dab-99d0-18a1cc3a8e99"}, "sec_annofile|annofile|annotations": {"id": "49223a3fae466eab", "src": "hda", "uuid": "7377a1eb-ee36-46a9-94b3-2a22648721cf"}}, "outputs": {"output_file": {"id": "4947f368a4a2c8df", "src": "hda", "uuid": "0b499c54-a360-42f1-856c-9d8e056c26d9"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-24 19:21:21", "plugin": "core", "name": "end_epoch", "raw_value": "1698175281.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:21:20", "plugin": "core", "name": "start_epoch", "raw_value": "1698175280.0000000"}, {"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/1.10-5", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.10", "test_index": 5, "time_seconds": 35.64164638519287, "inputs": {"input_file": {"src": "hda", "id": "94744cdca373f93e"}, "sec_annofile|columns": "ID,QUAL,FILTER,INFO,FMT", "sec_annofile|annofile|annotations": {"src": "hda", "id": "b792a00d371f877f"}, "sec_annofile|annofile|anno_fmt": "vcf", "sec_restrict|samples": "A", "output_type": "v"}, "job": {"model_class": "Job", "id": "732f42f4fdb7d4e8", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:22:06.989792", "create_time": "2023-10-24T19:21:53.001811", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10", "history_id": "ac0b688889bc6865", "external_id": "gxy-98p5w", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/0/6/dataset_f060b179-27c2-474a-83e0-b7a9dbd00602.dat' > input.vcf.gz && bcftools index input.vcf.gz && bgzip -c \"/galaxy/server/database/objects/9/2/1/dataset_9219916e-416e-49b8-b943-6586d596fcdc.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/4/0/c/dataset_40cab073-a0d1-428c-9a3e-862079477c08.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "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__\"}, \"samples\": \"A\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"\", \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 1, \"anno_fmt\": \"vcf\", \"annotations\": {\"values\": [{\"id\": 228, \"src\": \"hda\"}]}}, \"columns\": \"ID,QUAL,FILTER,INFO,FMT\", \"mark_sites\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "94744cdca373f93e", "src": "hda", "uuid": "f060b179-27c2-474a-83e0-b7a9dbd00602"}, "sec_annofile|annofile|annotations": {"id": "b792a00d371f877f", "src": "hda", "uuid": "9219916e-416e-49b8-b943-6586d596fcdc"}}, "outputs": {"output_file": {"id": "d784aead3274a7be", "src": "hda", "uuid": "40cab073-a0d1-428c-9a3e-862079477c08"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 19:21:55", "plugin": "core", "name": "end_epoch", "raw_value": "1698175315.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:21:55", "plugin": "core", "name": "start_epoch", "raw_value": "1698175315.0000000"}, {"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/1.10-6", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.10", "test_index": 6, "time_seconds": 31.191741228103638, "inputs": {"input_file": {"src": "hda", "id": "bd0b3ae80487f8af"}, "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": "1ca8b55c6d9ac19d", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:22:38.444427", "create_time": "2023-10-24T19:22:25.629754", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10", "history_id": "ac0b688889bc6865", "external_id": "gxy-dzpwc", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/0/e/dataset_f0e360a6-08d3-47d8-9b11-2c5d039e8fc4.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/4/5/0/dataset_450635d6-84f6-4fd7-ace2-af950dfe6d5e.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "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__\"}, \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL\", \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 0, \"anno_fmt\": \"none\"}, \"columns\": \"\", \"mark_sites\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "bd0b3ae80487f8af", "src": "hda", "uuid": "f0e360a6-08d3-47d8-9b11-2c5d039e8fc4"}}, "outputs": {"output_file": {"id": "0d472d3705ac1f23", "src": "hda", "uuid": "450635d6-84f6-4fd7-ace2-af950dfe6d5e"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 19:22:28", "plugin": "core", "name": "end_epoch", "raw_value": "1698175348.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:22:28", "plugin": "core", "name": "start_epoch", "raw_value": "1698175348.0000000"}, {"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/1.10-7", "has_data": true, "data": {"tool_id": "bcftools_annotate", "tool_version": "1.10", "test_index": 7, "time_seconds": 31.225550651550293, "inputs": {"input_file": {"src": "hda", "id": "7c84508ed18a5236"}, "sec_annofile|annofile|anno_fmt": "none", "sec_annotate|remove": "FORMAT", "output_type": "v"}, "job": {"model_class": "Job", "id": "eab6688cf88d7694", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:23:09.825915", "create_time": "2023-10-24T19:22:57.020173", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10", "history_id": "ac0b688889bc6865", "external_id": "gxy-jc55g", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/3/8/7/dataset_3875a861-6ca1-4439-bad5-1f908876af9d.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/c/2/e/dataset_c2e9af33-6536-41cb-8418-6055f4c42f95.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "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__\"}, \"samples\": \"\", \"samples_file\": null}", "sec_annotate": "{\"remove\": \"FORMAT\", \"rename_chrs\": null}", "sec_annofile": "{\"annofile\": {\"__current_case__\": 0, \"anno_fmt\": \"none\"}, \"columns\": \"\", \"mark_sites\": \"\", \"set_id\": \"\"}"}, "inputs": {"input_file": {"id": "7c84508ed18a5236", "src": "hda", "uuid": "3875a861-6ca1-4439-bad5-1f908876af9d"}}, "outputs": {"output_file": {"id": "d4588457f6d83c7b", "src": "hda", "uuid": "c2e9af33-6536-41cb-8418-6055f4c42f95"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-24 19:22:59", "plugin": "core", "name": "end_epoch", "raw_value": "1698175379.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:22:58", "plugin": "core", "name": "start_epoch", "raw_value": "1698175378.0000000"}, {"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/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.10", "test_index": 0, "time_seconds": 41.02406287193298, "inputs": {"input_files": [{"src": "hda", "id": "f0f09017b1d0df69"}, {"src": "hda", "id": "06e2b26b312abda8"}], "output_type": "v"}, "job": {"model_class": "Job", "id": "cfc5b7e266436803", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:17:10.858538", "create_time": "2023-10-24T19:16:51.346573", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10", "history_id": "ac0b688889bc6865", "external_id": "gxy-8697q", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/c/b/f/dataset_cbfe4a98-3db9-4160-8f3a-4f5a04fe5fa6.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/5/5/9/dataset_55929465-1f30-4188-9a2d-3d4e1ccefa8e.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/4/8/8/dataset_488feae3-8403-450f-bd26-993277f08369.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "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, \"naive\": \"no\", \"overlaps\": {\"__current_case__\": 0, \"allow_overlaps\": \"yes\", \"rm_dups\": null}}}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}}"}, "inputs": {"input_files1": {"id": "f0f09017b1d0df69", "src": "hda", "uuid": "cbfe4a98-3db9-4160-8f3a-4f5a04fe5fa6"}, "input_files": {"id": "f0f09017b1d0df69", "src": "hda", "uuid": "cbfe4a98-3db9-4160-8f3a-4f5a04fe5fa6"}, "input_files2": {"id": "06e2b26b312abda8", "src": "hda", "uuid": "55929465-1f30-4188-9a2d-3d4e1ccefa8e"}}, "outputs": {"output_file": {"id": "41830eb9b06130b5", "src": "hda", "uuid": "488feae3-8403-450f-bd26-993277f08369"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Checking the headers and starting positions of 2 files\n", "job_stdout": "", "job_stderr": "", "stderr": "Checking the headers and starting positions of 2 files\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-24 19:16:58", "plugin": "core", "name": "end_epoch", "raw_value": "1698175018.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:16:57", "plugin": "core", "name": "start_epoch", "raw_value": "1698175017.0000000"}, {"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/1.10-1", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.10", "test_index": 1, "time_seconds": 35.224337339401245, "inputs": {"input_files": [{"src": "hda", "id": "089c6cf9e80e4b36"}, {"src": "hda", "id": "a7428392cec995fb"}], "sec_default|mode|naive": "yes", "output_type": "v"}, "job": {"model_class": "Job", "id": "c3036908aaf65c65", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:17:46.500523", "create_time": "2023-10-24T19:17:32.321391", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10", "history_id": "ac0b688889bc6865", "external_id": "gxy-qj7d4", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/a/1/b/dataset_a1b4139b-a86e-4123-bf6a-79e12cf7213a.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/7/0/7/dataset_7078b037-b3be-47fa-86f2-176211daf306.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools concat --naive --min-PQ 30 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input0.vcf.gz input1.vcf.gz > output.gz && bcftools index output.gz && bcftools view -O v -o '/galaxy/server/database/objects/b/b/1/dataset_bb10508a-548e-4c8b-ab17-1986ebbf5aa9.dat' output.gz", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_default": "{\"compact_PS\": false, \"min_PQ\": \"30\", \"mode\": {\"__current_case__\": 0, \"naive\": \"yes\"}}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}}"}, "inputs": {"input_files": {"id": "089c6cf9e80e4b36", "src": "hda", "uuid": "a1b4139b-a86e-4123-bf6a-79e12cf7213a"}, "input_files1": {"id": "089c6cf9e80e4b36", "src": "hda", "uuid": "a1b4139b-a86e-4123-bf6a-79e12cf7213a"}, "input_files2": {"id": "a7428392cec995fb", "src": "hda", "uuid": "7078b037-b3be-47fa-86f2-176211daf306"}}, "outputs": {"output_file": {"id": "2a8bdd7c62d91aef", "src": "hda", "uuid": "bb10508a-548e-4c8b-ab17-1986ebbf5aa9"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Checking the headers of 2 files.\nDone, the headers are compatible.\nConcatenating input0.vcf.gz\t0.097559 seconds\nConcatenating input1.vcf.gz\t0.001170 seconds\n[W::vcf_parse] INFO 'XX' is not defined in the header, assuming Type=String\n[W::vcf_parse] FILTER 'Fail' is not defined in the header\n", "job_stdout": "", "job_stderr": "", "stderr": "Checking the headers of 2 files.\nDone, the headers are compatible.\nConcatenating input0.vcf.gz\t0.097559 seconds\nConcatenating input1.vcf.gz\t0.001170 seconds\n[W::vcf_parse] INFO 'XX' is not defined in the header, assuming Type=String\n[W::vcf_parse] FILTER 'Fail' is not defined in the header\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-24 19:17:35", "plugin": "core", "name": "end_epoch", "raw_value": "1698175055.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:17:34", "plugin": "core", "name": "start_epoch", "raw_value": "1698175054.0000000"}, {"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/1.10-2", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.10", "test_index": 2, "time_seconds": 11.822313785552979, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_concat/1.10-3", "has_data": true, "data": {"tool_id": "bcftools_concat", "tool_version": "1.10", "test_index": 3, "time_seconds": 33.625176668167114, "inputs": {"input_files": [{"src": "hda", "id": "991df7c395e355e3"}, {"src": "hda", "id": "7ac3c8ae18034e33"}], "sec_default|mode|overlaps|rm_dups": "none", "sec_default|mode|overlaps|allow_overlaps": "yes", "output_type": "v"}, "job": {"model_class": "Job", "id": "aac098e23e8cd7c2", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:18:31.921396", "create_time": "2023-10-24T19:18:19.304136", "galaxy_version": "23.1", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_concat/bcftools_concat/1.10", "history_id": "ac0b688889bc6865", "external_id": "gxy-mtss8", "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/c/8/5/dataset_c85d94db-9633-45be-8d2d-507991b36f25.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/2/0/d/dataset_20df871a-9cc3-47c8-a3db-506c9f1b567b.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/8/a/dataset_f8a56c14-bdc3-4fac-859d-43caa9eea7d6.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "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, \"naive\": \"no\", \"overlaps\": {\"__current_case__\": 0, \"allow_overlaps\": \"yes\", \"rm_dups\": \"none\"}}}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}}"}, "inputs": {"input_files": {"id": "991df7c395e355e3", "src": "hda", "uuid": "c85d94db-9633-45be-8d2d-507991b36f25"}, "input_files1": {"id": "991df7c395e355e3", "src": "hda", "uuid": "c85d94db-9633-45be-8d2d-507991b36f25"}, "input_files2": {"id": "7ac3c8ae18034e33", "src": "hda", "uuid": "20df871a-9cc3-47c8-a3db-506c9f1b567b"}}, "outputs": {"output_file": {"id": "10444dbe4484d9c4", "src": "hda", "uuid": "f8a56c14-bdc3-4fac-859d-43caa9eea7d6"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Checking the headers and starting positions of 2 files\n", "job_stdout": "", "job_stderr": "", "stderr": "Checking the headers and starting positions of 2 files\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 19:18:21", "plugin": "core", "name": "end_epoch", "raw_value": "1698175101.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:18:21", "plugin": "core", "name": "start_epoch", "raw_value": "1698175101.0000000"}, {"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": 37.91940975189209, "inputs": {"input_tabular": {"src": "hda", "id": "732f42f4fdb7d4e8"}, "key_column": "1"}, "job": {"model_class": "Job", "id": "e31e29894520e1d4", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:13:06.211455", "create_time": "2023-10-24T19:12:47.530478", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1", "history_id": "ac0b688889bc6865", "external_id": "gxy-jtthc", "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/5/7/d/dataset_57deed2d-9e31-4bab-b3f0-cdf0fc73fd04.dat' '/galaxy/server/database/objects/0/f/7/dataset_0f793180-54ce-4dcc-a041-ee602a25ead5.dat' '\t' '1'", "traceback": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "key_column": "\"1\""}, "inputs": {"input_tabular": {"id": "732f42f4fdb7d4e8", "src": "hda", "uuid": "57deed2d-9e31-4bab-b3f0-cdf0fc73fd04"}}, "outputs": {"output_tabular": {"id": "a8c4c29fd6e819a8", "src": "hda", "uuid": "0f793180-54ce-4dcc-a041-ee602a25ead5"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 19:12:55", "plugin": "core", "name": "end_epoch", "raw_value": "1698174775.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:12:55", "plugin": "core", "name": "start_epoch", "raw_value": "1698174775.0000000"}, {"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/tmppip0xu25out_1.tabular v. /tmp/tmpquxjjc64out_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/3.3.2.0.0-0", "has_data": true, "data": {"tool_id": "deeptools_compute_gc_bias", "tool_version": "3.3.2.0.0", "test_index": 0, "time_seconds": 68.51131963729858, "inputs": {"bamInput": {"src": "hda", "id": "8e1d8715b181df83"}, "source|input1": {"src": "hda", "id": "58c12ee26ed2e9fc"}, "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": "5bac8732f8a2ac76", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:35:28.735074", "create_time": "2023-10-24T18:34:42.240538", "galaxy_version": "23.1", "command_version": "computeGCBias 3.3.2", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.3.2.0.0", "history_id": "ac0b688889bc6865", "external_id": "gxy-4grj4", "command_line": "ln -s '/galaxy/server/database/objects/1/5/d/dataset_15d79519-d949-425e-9168-915b2d184c49.dat' local_bamInput.bam && ln -s '/galaxy/server/database/objects/_metadata_files/3/f/e/metadata_3fecfd30-38a4-43aa-b6e2-bde801a86289.dat' local_bamInput.bam.bai && computeGCBias --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bamfile local_bamInput.bam --GCbiasFrequenciesFile /galaxy/server/database/objects/f/a/4/dataset_fa4d8fd2-7f99-4c63-9ff3-4805b146ee3b.dat --fragmentLength 300 --genome /galaxy/server/database/objects/e/1/6/dataset_e16a8704-e076-477d-8c24-f0b21a57427e.dat --effectiveGenomeSize 10050 --region 'chr2L' --sampleSize '10' --regionSize '1'", "traceback": null, "params": {"source": "{\"__current_case__\": 1, \"input1\": {\"values\": [{\"id\": 10, \"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": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"source|input1": {"id": 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'/galaxy/server/database/objects/f/c/8/dataset_fc88b795-5cad-4a1d-8950-38f006628bb5.dat' '/galaxy/server/database/objects/0/c/6/dataset_0c629a63-df9e-4258-9616-3106a17a0980.dat' && cat run_info.json", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "pseudobam": "false", "lib_type": "\"\"", "fusion": "false", "seed": "\"42\"", "bootstrap_samples": "\"0\"", "bias": "false", "single_paired": "{\"__current_case__\": 1, \"collection\": {\"__current_case__\": 0, \"collection_selector\": \"datasets\", \"forward\": {\"values\": [{\"id\": 89, \"src\": \"hda\"}]}, \"reverse\": {\"values\": [{\"id\": 90, \"src\": \"hda\"}]}}, \"single_paired_selector\": \"paired\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 88, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": 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/galaxy/server/database/objects/f/c/8/dataset_fc88b795-5cad-4a1d-8950-38f006628bb5.dat /galaxy/server/database/objects/0/c/6/dataset_0c629a63-df9e-4258-9616-3106a17a0980.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/f/c/8/dataset_fc88b795-5cad-4a1d-8950-38f006628bb5.dat\n /galaxy/server/database/objects/0/c/6/dataset_0c629a63-df9e-4258-9616-3106a17a0980.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": "", "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/f/c/8/dataset_fc88b795-5cad-4a1d-8950-38f006628bb5.dat\n /galaxy/server/database/objects/0/c/6/dataset_0c629a63-df9e-4258-9616-3106a17a0980.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", "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\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 18:51:18 2023\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --threads 8 -o . /galaxy/server/database/objects/f/c/8/dataset_fc88b795-5cad-4a1d-8950-38f006628bb5.dat /galaxy/server/database/objects/0/c/6/dataset_0c629a63-df9e-4258-9616-3106a17a0980.dat\"\n}\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 18:51:18", "plugin": "core", "name": "end_epoch", "raw_value": "1698173478.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:51:18", "plugin": "core", "name": "start_epoch", "raw_value": "1698173478.0000000"}, {"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/0.46.0.4-1", "has_data": true, "data": {"tool_id": "kallisto_quant", "tool_version": "0.46.0.4", "test_index": 1, "time_seconds": 37.85233950614929, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "f0b5745d389aab92"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|collection|forward": {"src": "hda", "id": "7d10e1bf80f7a7b5"}, "single_paired|collection|reverse": {"src": "hda", "id": "4616f9c9a59bf3e9"}, "single_paired|collection|collection_selector": "datasets", "single_paired|single_paired_selector": "paired", "lib_type": "--fr-stranded"}, "job": {"model_class": "Job", "id": "74d2d2427b687a2d", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:52:07.647107", "create_time": "2023-10-24T18:51:55.564820", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4", "history_id": "ac0b688889bc6865", "external_id": "gxy-z4qs6", "command_line": "ln -s '/galaxy/server/database/objects/2/3/a/dataset_23afab59-3df4-4c7c-a2bb-6292c77e0e27.dat' reference.fa && kallisto index reference.fa -i reference.kallisto && kallisto quant -i 'reference.kallisto' --bootstrap-samples 0 --seed 42 --fr-stranded --threads ${GALAXY_SLOTS:-1} -o . '/galaxy/server/database/objects/2/1/b/dataset_21bd0854-b84e-4f71-978a-515ec7a30919.dat' '/galaxy/server/database/objects/8/7/3/dataset_873d26bc-4eb7-4e03-b428-e6e0f4bb5bad.dat' && cat run_info.json", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "pseudobam": "false", "lib_type": "\"--fr-stranded\"", "fusion": "false", "seed": "\"42\"", "bootstrap_samples": "\"0\"", "bias": "false", "single_paired": "{\"__current_case__\": 1, \"collection\": {\"__current_case__\": 0, \"collection_selector\": \"datasets\", \"forward\": {\"values\": [{\"id\": 94, \"src\": \"hda\"}]}, \"reverse\": {\"values\": [{\"id\": 95, \"src\": \"hda\"}]}}, \"single_paired_selector\": \"paired\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 93, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "f0b5745d389aab92", "src": "hda", "uuid": "23afab59-3df4-4c7c-a2bb-6292c77e0e27"}, "single_paired|collection|forward": {"id": "7d10e1bf80f7a7b5", "src": "hda", "uuid": "21bd0854-b84e-4f71-978a-515ec7a30919"}, "single_paired|collection|reverse": {"id": "4616f9c9a59bf3e9", "src": "hda", "uuid": "873d26bc-4eb7-4e03-b428-e6e0f4bb5bad"}}, "outputs": {"abundance_h5": {"id": "c6a87bf4e210abed", "src": "hda", "uuid": "f40fd688-0033-4111-999b-1316dcb16248"}, "abundance_tab": {"id": "0ba283993e024ac9", "src": "hda", "uuid": "e3d9fbb6-78b6-4d83-a192-6f8660bc1a56"}}, "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\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 18:51:57 2023\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --fr-stranded --threads 8 -o . /galaxy/server/database/objects/2/1/b/dataset_21bd0854-b84e-4f71-978a-515ec7a30919.dat /galaxy/server/database/objects/8/7/3/dataset_873d26bc-4eb7-4e03-b428-e6e0f4bb5bad.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/2/1/b/dataset_21bd0854-b84e-4f71-978a-515ec7a30919.dat\n /galaxy/server/database/objects/8/7/3/dataset_873d26bc-4eb7-4e03-b428-e6e0f4bb5bad.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": "", "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/2/1/b/dataset_21bd0854-b84e-4f71-978a-515ec7a30919.dat\n /galaxy/server/database/objects/8/7/3/dataset_873d26bc-4eb7-4e03-b428-e6e0f4bb5bad.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", "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\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 18:51:57 2023\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --fr-stranded --threads 8 -o . /galaxy/server/database/objects/2/1/b/dataset_21bd0854-b84e-4f71-978a-515ec7a30919.dat /galaxy/server/database/objects/8/7/3/dataset_873d26bc-4eb7-4e03-b428-e6e0f4bb5bad.dat\"\n}\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 18:51:57", "plugin": "core", "name": "end_epoch", "raw_value": "1698173517.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:51:57", "plugin": "core", "name": "start_epoch", "raw_value": "1698173517.0000000"}, {"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/0.46.0.4-2", "has_data": true, "data": {"tool_id": "kallisto_quant", "tool_version": "0.46.0.4", "test_index": 2, "time_seconds": 39.98147130012512, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "48d76540c42e811c"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|collection|reads": {"src": "hdca", "id": "5bac8732f8a2ac76"}, "single_paired|collection|collection_selector": "collection", "single_paired|single_paired_selector": "paired"}, "job": {"model_class": "Job", "id": "a7f4c64272513234", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:52:47.680514", "create_time": "2023-10-24T18:52:34.896741", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4", "history_id": "ac0b688889bc6865", "external_id": "gxy-dpnvz", "command_line": "ln -s '/galaxy/server/database/objects/4/0/7/dataset_407b6b0f-3df6-4177-88b3-33921dc571cb.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 . '/galaxy/server/database/objects/d/7/f/dataset_d7f6d1be-0d1c-42ca-afde-13a367103a03.dat' '/galaxy/server/database/objects/1/1/5/dataset_115f06b3-4b8d-459a-bca3-8ce85379b41d.dat' && cat run_info.json", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "pseudobam": "false", "lib_type": "\"\"", "fusion": "false", "seed": "\"42\"", "bootstrap_samples": "\"0\"", "bias": "false", "single_paired": "{\"__current_case__\": 1, \"collection\": {\"__current_case__\": 1, \"collection_selector\": \"collection\", \"reads\": {\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}}, \"single_paired_selector\": \"paired\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 98, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "48d76540c42e811c", "src": "hda", "uuid": "407b6b0f-3df6-4177-88b3-33921dc571cb"}, "single_paired|collection|reads1": {"id": "bd04633f9b0feeef", "src": "hda", "uuid": "d7f6d1be-0d1c-42ca-afde-13a367103a03"}, "single_paired|collection|reads2": {"id": "c8d9f9a5b2c5ead9", "src": "hda", "uuid": "115f06b3-4b8d-459a-bca3-8ce85379b41d"}}, "outputs": {"abundance_h5": {"id": "3155a4b1859c18a6", "src": "hda", "uuid": "827a827b-5501-4846-87a3-abdb44500f81"}, "abundance_tab": {"id": "524cb85cc9294f53", "src": "hda", "uuid": "e2c1388a-889a-4af6-9cec-5bb2b0a755ad"}}, "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\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 18:52:36 2023\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --threads 8 -o . /galaxy/server/database/objects/d/7/f/dataset_d7f6d1be-0d1c-42ca-afde-13a367103a03.dat /galaxy/server/database/objects/1/1/5/dataset_115f06b3-4b8d-459a-bca3-8ce85379b41d.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/d/7/f/dataset_d7f6d1be-0d1c-42ca-afde-13a367103a03.dat\n /galaxy/server/database/objects/1/1/5/dataset_115f06b3-4b8d-459a-bca3-8ce85379b41d.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": "", "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/d/7/f/dataset_d7f6d1be-0d1c-42ca-afde-13a367103a03.dat\n /galaxy/server/database/objects/1/1/5/dataset_115f06b3-4b8d-459a-bca3-8ce85379b41d.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", "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\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 18:52:36 2023\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --threads 8 -o . /galaxy/server/database/objects/d/7/f/dataset_d7f6d1be-0d1c-42ca-afde-13a367103a03.dat /galaxy/server/database/objects/1/1/5/dataset_115f06b3-4b8d-459a-bca3-8ce85379b41d.dat\"\n}\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 18:52:36", "plugin": "core", "name": "end_epoch", "raw_value": "1698173556.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:52:36", "plugin": "core", "name": "start_epoch", "raw_value": "1698173556.0000000"}, {"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/0.46.0.4-3", "has_data": true, "data": {"tool_id": "kallisto_quant", "tool_version": "0.46.0.4", "test_index": 3, "time_seconds": 34.347094774246216, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "1560ad2ca97a7aa4"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|reads": {"src": "hda", "id": "9438ffd2de4dad5d"}, "single_paired|single_paired_selector": "single"}, "job": {"model_class": "Job", "id": "bd64f0823b4de292", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:53:22.269391", "create_time": "2023-10-24T18:53:09.436895", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4", "history_id": "ac0b688889bc6865", "external_id": "gxy-hf8wv", "command_line": "ln -s '/galaxy/server/database/objects/6/2/8/dataset_628ccadc-b0bd-4b59-976e-a78d41dbd45c.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/a/4/3/dataset_a439e1d5-c36a-4d82-b90a-6ed3bb900204.dat' && cat run_info.json", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "pseudobam": "false", "lib_type": "\"\"", "fusion": "false", "seed": "\"42\"", "bootstrap_samples": "\"0\"", "bias": "false", "single_paired": "{\"__current_case__\": 0, \"fragment_length\": \"200\", \"reads\": {\"values\": [{\"id\": 104, \"src\": \"hda\"}]}, \"sd\": \"20\", \"single_paired_selector\": \"single\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 103, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "1560ad2ca97a7aa4", "src": "hda", "uuid": "628ccadc-b0bd-4b59-976e-a78d41dbd45c"}, "single_paired|reads": {"id": "9438ffd2de4dad5d", "src": "hda", "uuid": "a439e1d5-c36a-4d82-b90a-6ed3bb900204"}}, "outputs": {"abundance_h5": {"id": "9bcf99e4107f4237", "src": "hda", "uuid": "c7e6739e-fb97-4d25-bbfd-557427369c5b"}, "abundance_tab": {"id": "18bb15b43e20dd17", "src": "hda", "uuid": "5a5095ed-ec51-4564-bc29-ed63d998f111"}}, "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\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 18:53:11 2023\",\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/a/4/3/dataset_a439e1d5-c36a-4d82-b90a-6ed3bb900204.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/a/4/3/dataset_a439e1d5-c36a-4d82-b90a-6ed3bb900204.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": "", "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/a/4/3/dataset_a439e1d5-c36a-4d82-b90a-6ed3bb900204.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", "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\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 18:53:11 2023\",\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/a/4/3/dataset_a439e1d5-c36a-4d82-b90a-6ed3bb900204.dat\"\n}\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 18:53:11", "plugin": "core", "name": "end_epoch", "raw_value": "1698173591.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:53:11", "plugin": "core", "name": "start_epoch", "raw_value": "1698173591.0000000"}, {"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/0.46.0.4-4", "has_data": true, "data": {"tool_id": "kallisto_quant", "tool_version": "0.46.0.4", "test_index": 4, "time_seconds": 12.342719078063965, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "kallisto_quant/0.46.0.4-5", "has_data": true, "data": {"tool_id": "kallisto_quant", "tool_version": "0.46.0.4", "test_index": 5, "time_seconds": 20.787439584732056, "inputs": {"single_paired|collection|forward": {"src": "hda", "id": "1264ddbf04737629"}, "single_paired|collection|reverse": {"src": "hda", "id": "df7158a0b7e2c677"}, "single_paired|collection|collection_selector": "datasets", "single_paired|single_paired_selector": "paired", "pseudobam": true}, "execution_problem": "parameter 'index': an invalid option (None) was selected, please verify", "dynamic_param_error": true, "status": "error"}}, {"id": "kallisto_quant/0.46.0.4-6", "has_data": true, "data": {"tool_id": "kallisto_quant", "tool_version": "0.46.0.4", "test_index": 6, "time_seconds": 39.25564384460449, "inputs": {"reference_transcriptome|reference": {"src": "hda", "id": "ab59eac9aebdead2"}, "reference_transcriptome|reference_transcriptome_source": "history", "single_paired|collection|forward": {"src": "hda", "id": "bdd08e99baee49ac"}, "single_paired|collection|reverse": {"src": "hda", "id": "852ab0b15885923d"}, "single_paired|collection|collection_selector": "datasets", "single_paired|single_paired_selector": "paired", "fusion": true}, "job": {"model_class": "Job", "id": "8e54445da358ff67", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:54:34.614386", "create_time": "2023-10-24T18:54:21.620758", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4", "history_id": "ac0b688889bc6865", "external_id": "gxy-tdkx2", "command_line": "ln -s '/galaxy/server/database/objects/a/6/5/dataset_a65a6969-5e70-4701-a250-7b06096d169a.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/c/e/9/dataset_ce92c899-126d-4cdb-9f73-2b23c9a453f0.dat' '/galaxy/server/database/objects/b/e/c/dataset_bec61c3a-6221-49a4-a74c-1226b32f1dbf.dat' && cat run_info.json", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"hg38\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/hg38.len\"", "pseudobam": "false", "lib_type": "\"\"", "fusion": "true", "seed": "\"42\"", "bootstrap_samples": "\"0\"", "bias": "false", "single_paired": "{\"__current_case__\": 1, \"collection\": {\"__current_case__\": 0, \"collection_selector\": \"datasets\", \"forward\": {\"values\": [{\"id\": 113, \"src\": \"hda\"}]}, \"reverse\": {\"values\": [{\"id\": 114, \"src\": \"hda\"}]}}, \"single_paired_selector\": \"paired\"}", "reference_transcriptome": "{\"__current_case__\": 1, \"reference\": {\"values\": [{\"id\": 112, \"src\": \"hda\"}]}, \"reference_transcriptome_source\": \"history\"}"}, "inputs": {"reference_transcriptome|reference": {"id": "ab59eac9aebdead2", "src": "hda", "uuid": "a65a6969-5e70-4701-a250-7b06096d169a"}, "single_paired|collection|forward": {"id": "bdd08e99baee49ac", "src": "hda", "uuid": "ce92c899-126d-4cdb-9f73-2b23c9a453f0"}, "single_paired|collection|reverse": {"id": "852ab0b15885923d", "src": "hda", "uuid": "bec61c3a-6221-49a4-a74c-1226b32f1dbf"}}, "outputs": {"abundance_h5": {"id": "9f57a886f09cc2f6", "src": "hda", "uuid": "16c6540e-31c7-4ec1-ab36-153f78862773"}, "abundance_tab": {"id": "fcbdcf19b2b9f34a", "src": "hda", "uuid": "9d23b417-d6b8-4aa8-a215-d2cb613159ff"}, "fusion_output": {"id": "a311d08ab3542a74", "src": "hda", "uuid": "603899c3-442a-4ef1-97d7-5580f4e1e3d3"}}, "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\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 18:54:23 2023\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --fusion --threads 8 -o . /galaxy/server/database/objects/c/e/9/dataset_ce92c899-126d-4cdb-9f73-2b23c9a453f0.dat /galaxy/server/database/objects/b/e/c/dataset_bec61c3a-6221-49a4-a74c-1226b32f1dbf.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/c/e/9/dataset_ce92c899-126d-4cdb-9f73-2b23c9a453f0.dat\n /galaxy/server/database/objects/b/e/c/dataset_bec61c3a-6221-49a4-a74c-1226b32f1dbf.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": "", "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/c/e/9/dataset_ce92c899-126d-4cdb-9f73-2b23c9a453f0.dat\n /galaxy/server/database/objects/b/e/c/dataset_bec61c3a-6221-49a4-a74c-1226b32f1dbf.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", "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\": \"0.46.0\",\n\t\"index_version\": 10,\n\t\"start_time\": \"Tue Oct 24 18:54:23 2023\",\n\t\"call\": \"kallisto quant -i reference.kallisto --bootstrap-samples 0 --seed 42 --fusion --threads 8 -o . /galaxy/server/database/objects/c/e/9/dataset_ce92c899-126d-4cdb-9f73-2b23c9a453f0.dat /galaxy/server/database/objects/b/e/c/dataset_bec61c3a-6221-49a4-a74c-1226b32f1dbf.dat\"\n}\n", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-24 18:54:24", "plugin": "core", "name": "end_epoch", "raw_value": "1698173664.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:54:23", "plugin": "core", "name": "start_epoch", "raw_value": "1698173663.0000000"}, {"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": 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"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": "cb2e7127ce266030", "src": "hda", "uuid": "aca3f7ad-33ff-4572-9301-3af2dca0249d"}}, "outputs": {"output": {"id": "c737386f0a706b0e", "src": "hda", "uuid": "e227e498-bac1-4bec-9360-1eca02eb7de6"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 18:48:25", "plugin": "core", "name": "end_epoch", "raw_value": "1698173305.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:48:25", "plugin": "core", "name": "start_epoch", "raw_value": "1698173305.0000000"}, {"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+galaxy0-0", "has_data": true, "data": {"tool_id": "music_inspect_eset", "tool_version": "0.1.1+galaxy0", "test_index": 0, "time_seconds": 60.00078296661377, "inputs": {"rds_eset": {"src": "hda", "id": "d6b4c4af55b395bf"}, "inspector": "print"}, "job": {"model_class": "Job", "id": "1560ad2ca97a7aa4", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:59:50.117067", "create_time": "2023-10-24T18:59:09.082487", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-2ghwc", "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/000/103/configs/tmpq5u83zt6'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "inspector": "\"print\""}, "inputs": {"rds_eset": {"id": "d6b4c4af55b395bf", "src": "hda", "uuid": "f4eb0ecc-f6fa-4d92-882d-b894ecfe474c"}}, "outputs": {"out_tab": {"id": "8ba52912ae1e55db", "src": "hda", "uuid": "50239f34-fd9c-488f-97db-137252fd7a45"}}, "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": "", "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", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2023-10-24 18:59:34", "plugin": "core", "name": "end_epoch", "raw_value": "1698173974.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:59:29", "plugin": "core", "name": "start_epoch", "raw_value": "1698173969.0000000"}, {"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+galaxy0-0", "has_data": true, "data": {"tool_id": "music_inspect_eset", "tool_version": "0.1.1+galaxy0", "test_index": 0, "time_seconds": 37.70418572425842, "inputs": {"rds_eset": {"src": "hda", "id": "d5b0c18913f66bf3"}, "inspector": "print"}, "job": {"model_class": "Job", "id": "1330bcbd82a6e2e2", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:01:43.707785", "create_time": "2023-10-24T19:01:26.987086", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-s4hv5", "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/000/109/configs/tmpyc3z0j9k'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "inspector": "\"print\""}, "inputs": {"rds_eset": {"id": "d5b0c18913f66bf3", "src": "hda", "uuid": "f9e22075-bd5b-4495-9af1-6af40c4d918d"}}, "outputs": {"out_tab": {"id": "a954d7604bed494d", "src": "hda", "uuid": "6dad8ed5-333b-4434-8ca5-97e2fe63146e"}}, "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": "", "stderr": "", "stdout": "ExpressionSet (storageMode: lockedEnvironment)\nassayData: 2066 features, 250 samples \n element names: exprs \nprotocolData: none\nphenoData\n sampleNames: AZ_A10 AZ_A11 ... 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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 'fasta' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "traceback": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ignore_failed": "\"0\"", "molecule": "{\"__current_case__\": 0, \"format\": \"fasta\", \"select\": \"nucleotide\"}", "query_source": "{\"__current_case__\": 0, \"accession_file\": {\"values\": [{\"id\": 42, \"src\": \"hda\"}]}, \"select\": \"accession_file\"}"}, "inputs": {"query_source|accession_file": {"id": "173d64b18b61b79f", "src": "hda", "uuid": "7f5ec298-e991-47bc-a697-d35478649f9f"}}, "outputs": {"error_log": {"id": "06ef34d92aa036be", "src": "hda", "uuid": "7ac00f4b-dbce-4e61-803a-22d12a334689"}, "__new_primary_file_output|CP011064__": {"id": "4383aad762f80c46", "src": "hda", "uuid": "8fd7db34-b448-492e-ae22-1d22f903283f"}, "__new_primary_file_output|CP021680__": {"id": "598bb396b8283898", "src": "hda", "uuid": "a5eacd66-0f48-4e61-890c-3a3852f9aacd"}}, "output_collections": {"output": {"id": "ac0b688889bc6865", "src": "hdca"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}, {"title": "Job End Time", "value": "2023-10-24 18:43:54", "plugin": "core", "name": "end_epoch", "raw_value": "1698173034.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:43:48", "plugin": "core", "name": "start_epoch", "raw_value": "1698173028.0000000"}, {"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/0.2.5+galaxy0-1", "has_data": true, "data": {"tool_id": "ncbi_acc_download", "tool_version": "0.2.5+galaxy0", "test_index": 1, "time_seconds": 38.77350163459778, "inputs": {"query_source|accession_file": {"src": "hda", "id": "bc1061605e3dd270"}, "query_source|select": "accession_file", "molecule|format": "genbank", "molecule|select": "nucleotide"}, "job": {"model_class": "Job", "id": "598bb396b8283898", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:44:45.197711", "create_time": "2023-10-24T18:44:26.105270", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-bh5l9", "command_line": "{ grep -v \"^[ \\t]*$\" /galaxy/server/database/objects/b/e/b/dataset_bebfcfe4-3e12-44e7-a2ff-7151c8bb0a7c.dat > accessions || { echo \"No accession numbers in input. Aborting.\" 1>&2; exit 1; } } && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'genbank' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "traceback": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ignore_failed": "\"0\"", "molecule": "{\"__current_case__\": 0, \"format\": \"genbank\", \"select\": \"nucleotide\"}", "query_source": "{\"__current_case__\": 0, \"accession_file\": {\"values\": [{\"id\": 46, \"src\": \"hda\"}]}, \"select\": \"accession_file\"}"}, "inputs": {"query_source|accession_file": {"id": "bc1061605e3dd270", "src": "hda", "uuid": "bebfcfe4-3e12-44e7-a2ff-7151c8bb0a7c"}}, "outputs": {"error_log": {"id": "4874f2d88d284a15", "src": "hda", "uuid": "03452857-d5a1-4850-96b3-4403469a92b7"}, "__new_primary_file_output|CP011064__": {"id": "9565e53ed8fd0266", "src": "hda", "uuid": "53198e24-e656-4541-afd1-bdfa2cf32ae2"}, "__new_primary_file_output|CP021680__": {"id": "e4212d75cac01079", "src": "hda", "uuid": "dfc633ec-7906-400e-aeb5-2589208f0f2b"}}, "output_collections": {"output": {"id": "59f465c2df29f606", "src": "hdca"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "7 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "7.0000000"}, {"title": "Job End Time", "value": "2023-10-24 18:44:34", "plugin": "core", "name": "end_epoch", "raw_value": "1698173074.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:44:27", "plugin": "core", "name": "start_epoch", "raw_value": "1698173067.0000000"}, {"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/0.2.5+galaxy0-2", "has_data": true, "data": {"tool_id": "ncbi_acc_download", "tool_version": "0.2.5+galaxy0", "test_index": 2, "time_seconds": 39.00134611129761, "inputs": {"query_source|accession_file": {"src": "hda", "id": "c4a601c963c55414"}, "query_source|select": "accession_file", "molecule|format": "gff3", "molecule|select": "nucleotide"}, "job": {"model_class": "Job", "id": "4874f2d88d284a15", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:45:24.617550", "create_time": "2023-10-24T18:45:04.628579", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-8mg8b", "command_line": "{ grep -v \"^[ \\t]*$\" /galaxy/server/database/objects/7/d/d/dataset_7ddcc6ac-7d3b-4efb-9f46-230438411e62.dat > accessions || { echo \"No accession numbers in input. Aborting.\" 1>&2; exit 1; } } && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'gff3' ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "traceback": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ignore_failed": "\"0\"", "molecule": "{\"__current_case__\": 0, \"format\": \"gff3\", \"select\": \"nucleotide\"}", "query_source": "{\"__current_case__\": 0, \"accession_file\": {\"values\": [{\"id\": 50, \"src\": \"hda\"}]}, \"select\": \"accession_file\"}"}, "inputs": {"query_source|accession_file": {"id": "c4a601c963c55414", "src": "hda", "uuid": "7ddcc6ac-7d3b-4efb-9f46-230438411e62"}}, "outputs": {"error_log": {"id": "d7ee452aab829962", "src": "hda", "uuid": "6f46785b-bc29-4594-bf29-3e9160e9f736"}, "__new_primary_file_output|CP011064__": {"id": "9bd1d9c5aafa4abd", "src": "hda", "uuid": "a39f4089-a32b-405e-87cf-bf18791b4a4d"}, "__new_primary_file_output|CP021680__": {"id": "11f10f91ff4f160b", "src": "hda", "uuid": "ad2b5161-2cc0-42d9-a155-b1e006994c1e"}}, "output_collections": {"output": {"id": "0f03330fec4336c6", "src": "hdca"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "8 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "8.0000000"}, {"title": "Job End Time", "value": "2023-10-24 18:45:14", "plugin": "core", "name": "end_epoch", "raw_value": "1698173114.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:45:06", "plugin": "core", "name": "start_epoch", "raw_value": "1698173106.0000000"}, {"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/0.2.5+galaxy0-3", "has_data": true, "data": {"tool_id": "ncbi_acc_download", "tool_version": "0.2.5+galaxy0", "test_index": 3, "time_seconds": 37.849955797195435, "inputs": {"query_source|accession_file": {"src": "hda", "id": "b0fb798d32c218ee"}, "query_source|select": "accession_file", "molecule|format": "featuretable", "molecule|select": "nucleotide"}, "job": {"model_class": "Job", "id": "e4212d75cac01079", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:46:02.405518", "create_time": "2023-10-24T18:45:44.276701", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-vzwkf", "command_line": "{ grep -v \"^[ \\t]*$\" /galaxy/server/database/objects/b/4/d/dataset_b4db214b-0ddf-46ae-bf00-55f445bc0b40.dat > accessions || { echo \"No accession numbers in input. Aborting.\" 1>&2; exit 1; } } && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'featuretable' ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "traceback": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ignore_failed": "\"0\"", "molecule": "{\"__current_case__\": 0, \"format\": \"featuretable\", \"select\": \"nucleotide\"}", "query_source": "{\"__current_case__\": 0, \"accession_file\": {\"values\": [{\"id\": 54, \"src\": \"hda\"}]}, \"select\": \"accession_file\"}"}, "inputs": {"query_source|accession_file": {"id": "b0fb798d32c218ee", "src": "hda", "uuid": "b4db214b-0ddf-46ae-bf00-55f445bc0b40"}}, "outputs": {"error_log": {"id": "25a33fdcc7155303", "src": "hda", "uuid": "0eb7092a-29a7-417b-a5cf-8c51f86ff526"}, "__new_primary_file_output|CP011064__": {"id": "52ae05ee56bba40d", "src": "hda", "uuid": "43b36319-04e1-4d50-b9a8-68fc08faf9ee"}, "__new_primary_file_output|CP021680__": {"id": "39f64ffb6bb5a85d", "src": "hda", "uuid": "b53fdd3a-ad94-4e5b-ad00-7f499b6c7740"}}, "output_collections": {"output": {"id": "72253e6835b777d9", "src": "hdca"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}, {"title": "Job End Time", "value": "2023-10-24 18:45:51", "plugin": "core", "name": "end_epoch", "raw_value": "1698173151.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:45:45", "plugin": "core", "name": "start_epoch", "raw_value": "1698173145.0000000"}, {"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/0.2.5+galaxy0-4", "has_data": true, "data": {"tool_id": "ncbi_acc_download", "tool_version": "0.2.5+galaxy0", "test_index": 4, "time_seconds": 19.89552664756775, "inputs": {"query_source|accession_list": "CP011064,CP021680", "query_source|select": "accession_list", "molecule|format": "fasta", "molecule|select": "nucleotide"}, "job": {"model_class": "Job", "id": "c4a601c963c55414", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:46:22.724211", "create_time": "2023-10-24T18:46:04.219125", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-k27sr", "command_line": "echo 'CP011064,CP021680' | sed -r 's/(\\,|__cn__)/\\n/g' | grep -v \"^[ \\t]*$\" > accessions && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'fasta' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "traceback": null, "params": {"__input_ext": "\"data\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ignore_failed": "\"0\"", "molecule": "{\"__current_case__\": 0, \"format\": \"fasta\", \"select\": \"nucleotide\"}", "query_source": "{\"__current_case__\": 1, \"accession_list\": \"CP011064,CP021680\", \"select\": \"accession_list\"}"}, "inputs": {}, "outputs": {"error_log": {"id": "01b0f23a278b9e78", "src": "hda", "uuid": "670c3beb-77d9-4e5e-8a0b-d8dc337f5697"}, "__new_primary_file_output|CP011064__": {"id": "a9d5f919dd8b171d", "src": "hda", "uuid": "a3b03d8d-40e9-40b4-b94b-b06be60a857a"}, "__new_primary_file_output|CP021680__": {"id": "de93d291ffe03d8c", "src": "hda", "uuid": "b24ba4cb-20a5-4e53-b048-67630f87ad12"}}, "output_collections": {"output": {"id": "e5d9f713e948e834", "src": "hdca"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}, {"title": "Job End Time", "value": "2023-10-24 18:46:12", "plugin": "core", "name": "end_epoch", "raw_value": "1698173172.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:46:06", "plugin": "core", "name": "start_epoch", "raw_value": "1698173166.0000000"}, {"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/0.2.5+galaxy0-5", "has_data": true, "data": {"tool_id": "ncbi_acc_download", "tool_version": "0.2.5+galaxy0", "test_index": 5, "time_seconds": 23.973930597305298, "inputs": {"query_source|accession_list": "CP011064,CP0XXXXX,CP021680", "query_source|select": "accession_list", "molecule|format": "fasta", "molecule|select": "nucleotide", "ignore_failed": "1"}, "job": {"model_class": "Job", "id": "d7ee452aab829962", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:46:46.062153", "create_time": "2023-10-24T18:46:24.278345", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-2nwtj", "command_line": "echo 'CP011064,CP0XXXXX,CP021680' | sed -r 's/(\\,|__cn__)/\\n/g' | grep -v \"^[ \\t]*$\" > accessions && mkdir outdir && cd outdir && ignore_errors=1 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'fasta' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "traceback": null, "params": {"__input_ext": "\"data\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ignore_failed": "\"1\"", "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": "c629f0f0ba816e52", "src": "hda", "uuid": "43a1e401-4f81-4714-9144-48923a74cfc4"}, "failed_accessions": {"id": "090a7b7166038779", "src": "hda", "uuid": "c9de9fff-4905-43f0-aa3d-1bd6fcec5cdb"}, "__new_primary_file_output|CP011064__": {"id": "c40331942c13db2c", "src": "hda", "uuid": "32168d71-3c99-42c1-a470-836cf448c339"}, "__new_primary_file_output|CP021680__": {"id": "a5f0a445c5f454d5", "src": "hda", "uuid": "fb6236ed-0fb1-4f4b-82c5-a5849b42026d"}}, "output_collections": {"output": {"id": "26876408059cf80b", "src": "hdca"}}, "tool_stdout": "", "tool_stderr": "Failed to download file with id CP0XXXXX from NCBI\nTraceback (most recent call last):\n File \"/usr/local/bin/ncbi-acc-download\", line 10, in \n sys.exit(main())\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/__main__.py\", line 54, in main\n download_to_file(dl_id, config, filename, append)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/core.py\", line 110, in download_to_file\n r = get_stream(url, params)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/download.py\", line 90, in get_stream\n raise DownloadError(\"Download failed with return code: {}\".format(r.status_code))\nncbi_acc_download.errors.DownloadError: Download failed with return code: 400\n", "job_stdout": "", "job_stderr": "", "stderr": "Failed to download file with id CP0XXXXX from NCBI\nTraceback (most recent call last):\n File \"/usr/local/bin/ncbi-acc-download\", line 10, in \n sys.exit(main())\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/__main__.py\", line 54, in main\n download_to_file(dl_id, config, filename, append)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/core.py\", line 110, in download_to_file\n r = get_stream(url, params)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/download.py\", line 90, in get_stream\n raise DownloadError(\"Download failed with return code: {}\".format(r.status_code))\nncbi_acc_download.errors.DownloadError: Download failed with return code: 400\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "8 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "8.0000000"}, {"title": "Job End Time", "value": "2023-10-24 18:46:34", "plugin": "core", "name": "end_epoch", "raw_value": "1698173194.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:46:26", "plugin": "core", "name": "start_epoch", "raw_value": "1698173186.0000000"}, {"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/0.2.5+galaxy0-6", "has_data": true, "data": {"tool_id": "ncbi_acc_download", "tool_version": "0.2.5+galaxy0", "test_index": 6, "time_seconds": 17.510042428970337, "inputs": {"query_source|accession_list": "CP0XXXXX", "query_source|select": "accession_list", "molecule|format": "fasta", "molecule|select": "nucleotide", "ignore_failed": "1"}, "job": {"model_class": "Job", "id": "9bd1d9c5aafa4abd", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:47:04.486190", "create_time": "2023-10-24T18:46:48.404073", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-rqc94", "command_line": "echo 'CP0XXXXX' | sed -r 's/(\\,|__cn__)/\\n/g' | grep -v \"^[ \\t]*$\" > accessions && mkdir outdir && cd outdir && ignore_errors=1 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'fasta' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "traceback": null, "params": {"__input_ext": "\"data\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ignore_failed": "\"1\"", "molecule": "{\"__current_case__\": 0, \"format\": \"fasta\", \"select\": \"nucleotide\"}", "query_source": "{\"__current_case__\": 1, \"accession_list\": \"CP0XXXXX\", \"select\": \"accession_list\"}"}, "inputs": {}, "outputs": {"error_log": {"id": "cfc3093e0769cd96", "src": "hda", "uuid": "ac047c90-683b-4b32-99ef-ba0324bfce3f"}, "failed_accessions": {"id": "8c84a29f56b0f280", "src": "hda", "uuid": "9a4a2137-3689-43a1-b6e4-40bb3eddaf5a"}}, "output_collections": {"output": {"id": "768799d0c94cf0ff", "src": "hdca"}}, "tool_stdout": "", "tool_stderr": "Failed to download file with id CP0XXXXX from NCBI\nTraceback (most recent call last):\n File \"/usr/local/bin/ncbi-acc-download\", line 10, in \n sys.exit(main())\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/__main__.py\", line 54, in main\n download_to_file(dl_id, config, filename, append)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/core.py\", line 110, in download_to_file\n r = get_stream(url, params)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/download.py\", line 90, in get_stream\n raise DownloadError(\"Download failed with return code: {}\".format(r.status_code))\nncbi_acc_download.errors.DownloadError: Download failed with return code: 400\n", "job_stdout": "", "job_stderr": "", "stderr": "Failed to download file with id CP0XXXXX from NCBI\nTraceback (most recent call last):\n File \"/usr/local/bin/ncbi-acc-download\", line 10, in \n sys.exit(main())\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/__main__.py\", line 54, in main\n download_to_file(dl_id, config, filename, append)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/core.py\", line 110, in download_to_file\n r = get_stream(url, params)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/download.py\", line 90, in get_stream\n raise DownloadError(\"Download failed with return code: {}\".format(r.status_code))\nncbi_acc_download.errors.DownloadError: Download failed with return code: 400\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2023-10-24 18:46:53", "plugin": "core", "name": "end_epoch", "raw_value": "1698173213.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:46:50", "plugin": "core", "name": "start_epoch", "raw_value": "1698173210.0000000"}, {"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/0.2.5+galaxy0-7", "has_data": true, "data": {"tool_id": "ncbi_acc_download", "tool_version": "0.2.5+galaxy0", "test_index": 7, "time_seconds": 17.39913058280945, "inputs": {"query_source|accession_list": "CP011064,CP0XXXXX,CP021680", "query_source|select": "accession_list", "molecule|format": "fasta", "molecule|select": "nucleotide", "ignore_failed": "0"}, "job": {"model_class": "Job", "id": "11f10f91ff4f160b", "state": "error", "exit_code": 1, "update_time": "2023-10-24T18:47:22.553600", "create_time": "2023-10-24T18:47:06.070631", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-fzxjc", "command_line": "echo 'CP011064,CP0XXXXX,CP021680' | sed -r 's/(\\,|__cn__)/\\n/g' | grep -v \"^[ \\t]*$\" > accessions && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'fasta' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "traceback": null, "params": {"__input_ext": "\"data\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ignore_failed": "\"0\"", "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": "799d0bfb7f1bdb54", "src": "hda", "uuid": "d1c94233-5843-4d39-a5a8-6f74648f9e7c"}, "__new_primary_file_output|CP011064__": {"id": "5b2f017fabdab700", "src": "hda", "uuid": "43f58e33-fab1-49ac-a8e6-09d650c448ba"}}, "output_collections": {"output": {"id": "b9bef7d910419ef5", "src": "hdca"}}, "tool_stdout": "", "tool_stderr": "Failed to download file with id CP0XXXXX from NCBI\nTraceback (most recent call last):\n File \"/usr/local/bin/ncbi-acc-download\", line 10, in \n sys.exit(main())\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/__main__.py\", line 54, in main\n download_to_file(dl_id, config, filename, append)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/core.py\", line 110, in download_to_file\n r = get_stream(url, params)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/download.py\", line 90, in get_stream\n raise DownloadError(\"Download failed with return code: {}\".format(r.status_code))\nncbi_acc_download.errors.DownloadError: Download failed with return code: 400\n", "job_stdout": "", "job_stderr": "", "stderr": "Failed to download file with id CP0XXXXX from NCBI\nTraceback (most recent call last):\n File \"/usr/local/bin/ncbi-acc-download\", line 10, in \n sys.exit(main())\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/__main__.py\", line 54, in main\n download_to_file(dl_id, config, filename, append)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/core.py\", line 110, in download_to_file\n r = get_stream(url, params)\n File \"/usr/local/lib/python3.8/site-packages/ncbi_acc_download/download.py\", line 90, in get_stream\n raise DownloadError(\"Download failed with return code: {}\".format(r.status_code))\nncbi_acc_download.errors.DownloadError: Download failed with return code: 400\n", "stdout": "", "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2023-10-24 18:47:11", "plugin": "core", "name": "end_epoch", "raw_value": "1698173231.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:47:08", "plugin": "core", "name": "start_epoch", "raw_value": "1698173228.0000000"}, {"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/0.2.5+galaxy0-8", "has_data": true, "data": {"tool_id": "ncbi_acc_download", "tool_version": "0.2.5+galaxy0", "test_index": 8, "time_seconds": 19.88876175880432, "inputs": {"query_source|accession_list": "CP011064\nCP021680", "query_source|select": "accession_list", "molecule|format": "fasta", "molecule|select": "nucleotide"}, "job": {"model_class": "Job", "id": "b0fb798d32c218ee", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:47:41.772733", "create_time": "2023-10-24T18:47:23.630085", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-2d5j8", "command_line": "echo 'CP011064__cn__CP021680' | sed -r 's/(\\,|__cn__)/\\n/g' | grep -v \"^[ \\t]*$\" > accessions && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'fasta' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "traceback": null, "params": {"__input_ext": "\"data\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ignore_failed": "\"0\"", "molecule": "{\"__current_case__\": 0, \"format\": \"fasta\", \"select\": \"nucleotide\"}", "query_source": "{\"__current_case__\": 1, \"accession_list\": \"CP011064\\nCP021680\", \"select\": \"accession_list\"}"}, "inputs": {}, "outputs": {"error_log": {"id": "74d2d2427b687a2d", "src": "hda", "uuid": "9dff47c8-ad51-4aa4-8db5-04eeaee4cea2"}, "__new_primary_file_output|CP011064__": {"id": "7685238fb7b04c15", "src": "hda", "uuid": "f82d6e1c-6e64-4af9-b81f-4e574f083e8b"}, "__new_primary_file_output|CP021680__": {"id": "7c9aa62e97999166", "src": "hda", "uuid": "c0165fa8-9b7c-4396-852c-4d174040f9e1"}}, "output_collections": {"output": {"id": "8e1d8715b181df83", "src": "hdca"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}, {"title": "Job End Time", "value": "2023-10-24 18:47:31", "plugin": "core", "name": "end_epoch", "raw_value": "1698173251.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:47:25", "plugin": "core", "name": "start_epoch", "raw_value": "1698173245.0000000"}, {"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/0.2.5+galaxy0-9", "has_data": true, "data": {"tool_id": "ncbi_acc_download", "tool_version": "0.2.5+galaxy0", "test_index": 9, "time_seconds": 16.438409090042114, "inputs": {"query_source|accession_list": "NP_003192", "query_source|select": "accession_list", "molecule|format": "fasta", "molecule|select": "protein"}, "job": {"model_class": "Job", "id": "25a33fdcc7155303", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:47:58.941200", "create_time": "2023-10-24T18:47:43.675630", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-5s5m7", "command_line": "echo 'NP_003192' | 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 'protein' --format 'fasta' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", "traceback": null, "params": {"__input_ext": "\"data\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "ignore_failed": "\"0\"", "molecule": "{\"__current_case__\": 1, \"format\": \"fasta\", \"select\": \"protein\"}", "query_source": "{\"__current_case__\": 1, \"accession_list\": \"NP_003192\", \"select\": \"accession_list\"}"}, "inputs": {}, "outputs": {"error_log": {"id": "aa2d44014a2b77b9", "src": "hda", "uuid": "db8ae373-e227-4863-b266-4392163f8243"}, "__new_primary_file_output|NP_003192__": {"id": "a7f4c64272513234", "src": "hda", "uuid": "262cb9ea-2b5b-4252-8aa8-ed61d7c8e36c"}}, "output_collections": {"output": {"id": "58c12ee26ed2e9fc", "src": "hdca"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2023-10-24 18:47:48", "plugin": "core", "name": "end_epoch", "raw_value": "1698173268.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:47:45", "plugin": "core", "name": "start_epoch", "raw_value": "1698173265.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "poretools_squiggle/0.6.1a1.1-0", "has_data": true, "data": {"tool_id": "poretools_squiggle", "tool_version": "0.6.1a1.1", "test_index": 0, "time_seconds": 80.96996712684631, "inputs": {"input": {"src": "hda", "id": "bd64f0823b4de292"}, "extension": "png"}, "job": {"model_class": "Job", "id": "a9d5f919dd8b171d", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:49:59.099528", "create_time": "2023-10-24T18:49:01.492370", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.1", "history_id": "ac0b688889bc6865", "external_id": "gxy-njs6t", "command_line": "export MPLBACKEND=\"agg\" && poretools squiggle '/galaxy/server/database/objects/2/d/2/dataset_2d22d967-58b8-4bc7-a402-daef44aabc70.dat' --saveas png --num-facets 6", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "num_facets": "\"6\"", "theme_bw": "false", "extension": "\"png\""}, "inputs": {"input": {"id": "bd64f0823b4de292", "src": "hda", "uuid": "2d22d967-58b8-4bc7-a402-daef44aabc70"}}, "outputs": {"output": {"id": "1486d3c4f6725a5b", "src": "hda", "uuid": "4a49878a-7be1-4254-83b5-e68d2e75ff6f"}, "__new_primary_file_output|2016_3_4_3507_1_ch126_read1377_strand.fast5__": {"id": "a043e6313ba48540", "src": "hda", "uuid": "7a667f21-9c69-4cdc-a4bc-997f3906bd08"}, "__new_primary_file_output|2016_3_4_3507_1_ch126_read326_strand.fast5__": {"id": "e3188b4015d44fa9", "src": "hda", "uuid": "1e5a6714-99c4-45ef-83b9-501746f2a3fc"}, "__new_primary_file_output|2016_3_4_3507_1_ch128_read430_strand.fast5__": {"id": "84b01522a8cd0c4c", "src": "hda", "uuid": "b91666bc-36a6-44ce-a343-58d72203ec08"}, "__new_primary_file_output|2016_3_4_3507_1_ch128_read95_strand.fast5__": {"id": "0e133955a3a6752a", "src": "hda", "uuid": "4838e004-a97c-4849-ae4c-fdab464174dc"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "13 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "13.0000000"}, {"title": "Job End Time", "value": "2023-10-24 18:49:41", "plugin": "core", "name": "end_epoch", "raw_value": 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'/galaxy/server/database/jobs_directory/000/137/configs/tmpjwa17kuw' &> '/galaxy/server/database/objects/1/f/b/dataset_1fb8bd2b-1c99-4aaf-8459-8f7e66ee97bb.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "diffgtest": "{\"__current_case__\": 1, \"do_opt\": \"yes\", \"set_a\": {\"meth\": {\"__current_case__\": 0, \"selector\": \"1,2\", \"type\": \"cln\"}, \"name_set\": \"Test set A\"}, \"set_b\": {\"meth\": {\"__current_case__\": 0, \"selector\": \"3,4,6\", \"type\": \"cln\"}, \"name_set\": \"Test set B\"}, \"use\": {\"__current_case__\": 0, \"def\": \"yes\"}}", "gois": "{\"__current_case__\": 0, \"do_opt\": \"no\"}", "plotsym": "{\"__current_case__\": 0, \"do_opt\": \"no\"}", "plotgen": "{\"__current_case__\": 1, \"clusts_plot\": \"\", \"do_opt\": \"yes\"}"}, "inputs": {"inputrds": {"id": "c618c8b87838dbd1", "src": "hda", "uuid": "d15baf50-880d-4089-8077-4912d05b5ab6"}}, "outputs": {"outpdf": {"id": "0485679c2ee3e895", "src": "hda", "uuid": "d9a24a23-a107-453a-890d-1e42fd11fd43"}, "outlog": {"id": "f750772d912e725f", "src": "hda", "uuid": "1fb8bd2b-1c99-4aaf-8459-8f7e66ee97bb"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2023-10-24 19:10:40", "plugin": "core", "name": "end_epoch", "raw_value": "1698174640.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:10:36", "plugin": "core", "name": "start_epoch", "raw_value": "1698174636.0000000"}, {"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/1.4.13-0", "has_data": true, "data": {"tool_id": "racon", "tool_version": "1.4.13", "test_index": 0, "time_seconds": 132.45905184745789, "inputs": {"reads": {"src": "hda", "id": "ac0b688889bc6865"}, "overlaps": {"src": "hda", "id": "59f465c2df29f606"}, "corrected_reads": {"src": "hda", "id": "0f03330fec4336c6"}, "u": true, "f": true, "w": "800", "e": "0.2"}, "job": {"model_class": "Job", "id": "72253e6835b777d9", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:33:40.566495", "create_time": "2023-10-24T18:32:23.478191", "galaxy_version": "23.1", "command_version": "v1.4.13", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13", "history_id": "ac0b688889bc6865", "external_id": "gxy-9cqc4", "command_line": "ln -s '/galaxy/server/database/objects/3/9/3/dataset_393a917f-e123-48da-8c5b-9aded2adc87e.dat' reads.fasta && ln -s '/galaxy/server/database/objects/8/8/0/dataset_8805a638-bc3e-4b08-9d77-d2d399229289.dat' overlaps.sam && ln -s '/galaxy/server/database/objects/9/d/8/dataset_9d824dbe-857f-43c1-a319-cf582b5300e2.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 5 -x -4 -g -8 > racon_polished_consensus.fa", "traceback": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "g": "\"-8\"", "x": "\"-4\"", "m": "\"5\"", "e": "\"0.2\"", "q": "\"10.0\"", "w": "\"800\"", "f": "true", "u": "true"}, "inputs": {"corrected_reads": {"id": "0f03330fec4336c6", "src": "hda", "uuid": "9d824dbe-857f-43c1-a319-cf582b5300e2"}, "overlaps": {"id": "59f465c2df29f606", "src": "hda", "uuid": "8805a638-bc3e-4b08-9d77-d2d399229289"}, "reads": {"id": "ac0b688889bc6865", "src": "hda", "uuid": "393a917f-e123-48da-8c5b-9aded2adc87e"}}, "outputs": {"consensus": {"id": "72253e6835b777d9", "src": "hda", "uuid": "058c453f-c13f-462c-b6df-6cb9be79bfd3"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[racon::Polisher::initialize] loaded target sequences 0.000895 s\n[racon::Polisher::initialize] loaded sequences 0.012984 s\n[racon::Polisher::initialize] loaded overlaps 0.012603 s\n[racon::Polisher::initialize] aligning overlaps [=> ] 0.003563 s\r[racon::Polisher::initialize] aligning overlaps [==> ] 0.003584 s\r[racon::Polisher::initialize] aligning overlaps [===> ] 0.003688 s\r[racon::Polisher::initialize] aligning overlaps [====> ] 0.005533 s\r[racon::Polisher::initialize] aligning overlaps [=====> ] 0.005550 s\r[racon::Polisher::initialize] aligning overlaps [======> ] 0.005560 s\r[racon::Polisher::initialize] aligning overlaps [=======> ] 0.005570 s\r[racon::Polisher::initialize] aligning overlaps [========> ] 0.005581 s\r[racon::Polisher::initialize] aligning overlaps [=========> ] 0.005591 s\r[racon::Polisher::initialize] aligning overlaps [==========> ] 0.005602 s\r[racon::Polisher::initialize] aligning overlaps [===========> ] 0.005612 s\r[racon::Polisher::initialize] aligning overlaps [============> ] 0.005622 s\r[racon::Polisher::initialize] aligning overlaps [=============> ] 0.005632 s\r[racon::Polisher::initialize] aligning overlaps [==============> ] 0.005643 s\r[racon::Polisher::initialize] aligning overlaps [===============> ] 0.005653 s\r[racon::Polisher::initialize] aligning overlaps [================> ] 0.005663 s\r[racon::Polisher::initialize] aligning overlaps [=================> ] 0.005674 s\r[racon::Polisher::initialize] aligning overlaps [==================> ] 0.005684 s\r[racon::Polisher::initialize] aligning overlaps [===================>] 0.005695 s\r[racon::Polisher::initialize] aligning overlaps [====================] 0.005705 s\n[racon::Polisher::initialize] transformed data into windows 0.000330 s\n[racon::Polisher::polish] generating consensus [=> ] 0.099324 s\r[racon::Polisher::polish] generating consensus [==> ] 0.099368 s\r[racon::Polisher::polish] generating consensus [===> ] 0.099397 s\r[racon::Polisher::polish] generating consensus [====> ] 0.101504 s\r[racon::Polisher::polish] generating consensus [=====> ] 0.105243 s\r[racon::Polisher::polish] generating consensus [======> ] 0.125058 s\r[racon::Polisher::polish] generating consensus [=======> ] 0.140161 s\r[racon::Polisher::polish] generating consensus [========> ] 0.174749 s\r[racon::Polisher::polish] generating consensus [=========> ] 0.213913 s\r[racon::Polisher::polish] generating consensus [==========> ] 0.238018 s\r[racon::Polisher::polish] generating consensus [===========> ] 0.316152 s\r[racon::Polisher::polish] generating consensus [============> ] 0.316945 s\r[racon::Polisher::polish] generating consensus [=============> ] 0.350444 s\r[racon::Polisher::polish] generating consensus [==============> ] 0.392238 s\r[racon::Polisher::polish] generating consensus [===============> ] 0.392391 s\r[racon::Polisher::polish] generating consensus [================> ] 0.443380 s\r[racon::Polisher::polish] generating consensus [=================> ] 0.443424 s\r[racon::Polisher::polish] generating consensus [==================> ] 0.467153 s\r[racon::Polisher::polish] generating consensus [===================>] 0.493275 s\r[racon::Polisher::polish] generating consensus [====================] 0.509450 s\n[racon::Polisher::] total = 0.546181 s\n", "job_stdout": "", "job_stderr": "", "stderr": "[racon::Polisher::initialize] loaded target sequences 0.000895 s\n[racon::Polisher::initialize] loaded sequences 0.012984 s\n[racon::Polisher::initialize] loaded overlaps 0.012603 s\n[racon::Polisher::initialize] aligning overlaps [=> ] 0.003563 s\r[racon::Polisher::initialize] aligning overlaps [==> ] 0.003584 s\r[racon::Polisher::initialize] aligning overlaps [===> ] 0.003688 s\r[racon::Polisher::initialize] aligning overlaps [====> ] 0.005533 s\r[racon::Polisher::initialize] aligning overlaps [=====> ] 0.005550 s\r[racon::Polisher::initialize] aligning overlaps [======> ] 0.005560 s\r[racon::Polisher::initialize] aligning overlaps [=======> ] 0.005570 s\r[racon::Polisher::initialize] aligning overlaps [========> ] 0.005581 s\r[racon::Polisher::initialize] aligning overlaps [=========> ] 0.005591 s\r[racon::Polisher::initialize] aligning overlaps [==========> ] 0.005602 s\r[racon::Polisher::initialize] aligning overlaps [===========> ] 0.005612 s\r[racon::Polisher::initialize] aligning overlaps [============> ] 0.005622 s\r[racon::Polisher::initialize] aligning overlaps [=============> ] 0.005632 s\r[racon::Polisher::initialize] aligning overlaps [==============> ] 0.005643 s\r[racon::Polisher::initialize] aligning overlaps [===============> ] 0.005653 s\r[racon::Polisher::initialize] aligning overlaps [================> ] 0.005663 s\r[racon::Polisher::initialize] aligning overlaps [=================> ] 0.005674 s\r[racon::Polisher::initialize] aligning overlaps [==================> ] 0.005684 s\r[racon::Polisher::initialize] aligning overlaps [===================>] 0.005695 s\r[racon::Polisher::initialize] aligning overlaps [====================] 0.005705 s\n[racon::Polisher::initialize] transformed data into windows 0.000330 s\n[racon::Polisher::polish] generating consensus [=> ] 0.099324 s\r[racon::Polisher::polish] generating consensus [==> ] 0.099368 s\r[racon::Polisher::polish] generating consensus [===> ] 0.099397 s\r[racon::Polisher::polish] generating consensus [====> ] 0.101504 s\r[racon::Polisher::polish] generating consensus [=====> ] 0.105243 s\r[racon::Polisher::polish] generating consensus [======> ] 0.125058 s\r[racon::Polisher::polish] generating consensus [=======> ] 0.140161 s\r[racon::Polisher::polish] generating consensus [========> ] 0.174749 s\r[racon::Polisher::polish] generating consensus [=========> ] 0.213913 s\r[racon::Polisher::polish] generating consensus [==========> ] 0.238018 s\r[racon::Polisher::polish] generating consensus [===========> ] 0.316152 s\r[racon::Polisher::polish] generating consensus [============> ] 0.316945 s\r[racon::Polisher::polish] generating consensus [=============> ] 0.350444 s\r[racon::Polisher::polish] generating consensus [==============> ] 0.392238 s\r[racon::Polisher::polish] generating consensus [===============> ] 0.392391 s\r[racon::Polisher::polish] generating consensus [================> ] 0.443380 s\r[racon::Polisher::polish] generating consensus [=================> ] 0.443424 s\r[racon::Polisher::polish] generating consensus [==================> ] 0.467153 s\r[racon::Polisher::polish] generating consensus [===================>] 0.493275 s\r[racon::Polisher::polish] generating consensus [====================] 0.509450 s\n[racon::Polisher::] total = 0.546181 s\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2023-10-24 18:33:29", "plugin": "core", "name": "end_epoch", "raw_value": "1698172409.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:33:28", "plugin": "core", "name": "start_epoch", "raw_value": "1698172408.0000000"}, {"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/1.4.13-1", "has_data": true, "data": {"tool_id": "racon", "tool_version": "1.4.13", "test_index": 1, "time_seconds": 37.794944047927856, "inputs": {"reads": {"src": "hda", "id": "e5d9f713e948e834"}, "overlaps": {"src": "hda", "id": "26876408059cf80b"}, "corrected_reads": {"src": "hda", "id": "768799d0c94cf0ff"}}, "job": {"model_class": "Job", "id": "b9bef7d910419ef5", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:34:18.524412", "create_time": "2023-10-24T18:34:06.280848", "galaxy_version": "23.1", "command_version": "v1.4.13", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13", "history_id": "ac0b688889bc6865", "external_id": "gxy-d2d6n", "command_line": "ln -s '/galaxy/server/database/objects/6/9/d/dataset_69d5fb53-c733-4b6c-bc6c-112a17d0018c.dat' reads.fasta && ln -s '/galaxy/server/database/objects/f/1/8/dataset_f18f3c7e-089a-4577-952a-131665726a4f.dat' overlaps.paf && ln -s '/galaxy/server/database/objects/7/1/d/dataset_71d09aa1-0ca0-4626-bd10-f9725bce1468.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 5 -x -4 -g -8 > racon_polished_consensus.fa", "traceback": null, "params": {"u": "false", "f": "false", "w": "\"500\"", "q": "\"10.0\"", "e": "\"0.3\"", "m": "\"5\"", "x": "\"-4\"", "g": "\"-8\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fasta\""}, "inputs": {"corrected_reads": {"id": "768799d0c94cf0ff", "src": "hda", "uuid": "71d09aa1-0ca0-4626-bd10-f9725bce1468"}, "overlaps": {"id": "26876408059cf80b", "src": "hda", "uuid": "f18f3c7e-089a-4577-952a-131665726a4f"}, "reads": {"id": "e5d9f713e948e834", "src": "hda", "uuid": "69d5fb53-c733-4b6c-bc6c-112a17d0018c"}}, "outputs": {"consensus": {"id": "b9bef7d910419ef5", "src": "hda", "uuid": "a3b85cfc-99fe-463d-95d6-d0801a9ce099"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[racon::Polisher::initialize] loaded target sequences 0.001212 s\n[racon::Polisher::initialize] loaded sequences 0.015353 s\n[racon::Polisher::initialize] loaded overlaps 0.000635 s\n[racon::Polisher::initialize] aligning overlaps [=> ] 0.023210 s\r[racon::Polisher::initialize] aligning overlaps [==> ] 0.033253 s\r[racon::Polisher::initialize] aligning overlaps [===> ] 0.034746 s\r[racon::Polisher::initialize] aligning overlaps [====> ] 0.037507 s\r[racon::Polisher::initialize] aligning overlaps [=====> ] 0.056783 s\r[racon::Polisher::initialize] aligning overlaps [======> ] 0.056866 s\r[racon::Polisher::initialize] aligning overlaps [=======> ] 0.059320 s\r[racon::Polisher::initialize] aligning overlaps [========> ] 0.067356 s\r[racon::Polisher::initialize] aligning overlaps [=========> ] 0.079894 s\r[racon::Polisher::initialize] aligning overlaps [==========> ] 0.082588 s\r[racon::Polisher::initialize] aligning overlaps [===========> ] 0.086414 s\r[racon::Polisher::initialize] aligning overlaps [============> ] 0.092322 s\r[racon::Polisher::initialize] aligning overlaps [=============> ] 0.105871 s\r[racon::Polisher::initialize] aligning overlaps [==============> ] 0.106335 s\r[racon::Polisher::initialize] aligning overlaps [===============> ] 0.116799 s\r[racon::Polisher::initialize] aligning overlaps [================> ] 0.128586 s\r[racon::Polisher::initialize] aligning overlaps [=================> ] 0.128676 s\r[racon::Polisher::initialize] aligning overlaps [==================> ] 0.134370 s\r[racon::Polisher::initialize] aligning overlaps [===================>] 0.137779 s\r[racon::Polisher::initialize] aligning overlaps [====================] 0.156020 s\n[racon::Polisher::initialize] transformed data into windows 0.000433 s\n[racon::Polisher::polish] generating consensus [=> ] 0.027790 s\r[racon::Polisher::polish] generating consensus [==> ] 0.027881 s\r[racon::Polisher::polish] generating consensus [===> ] 0.042281 s\r[racon::Polisher::polish] generating consensus [====> ] 0.042387 s\r[racon::Polisher::polish] generating consensus [=====> ] 0.049526 s\r[racon::Polisher::polish] generating consensus [======> ] 0.051153 s\r[racon::Polisher::polish] generating consensus [=======> ] 0.057800 s\r[racon::Polisher::polish] generating consensus [========> ] 0.061971 s\r[racon::Polisher::polish] generating consensus [=========> ] 0.069788 s\r[racon::Polisher::polish] generating consensus [==========> ] 0.082611 s\r[racon::Polisher::polish] generating consensus [===========> ] 0.103810 s\r[racon::Polisher::polish] generating consensus [============> ] 0.110494 s\r[racon::Polisher::polish] generating consensus [=============> ] 0.144806 s\r[racon::Polisher::polish] generating consensus [==============> ] 0.151725 s\r[racon::Polisher::polish] generating consensus [===============> ] 0.176979 s\r[racon::Polisher::polish] generating consensus [================> ] 0.179273 s\r[racon::Polisher::polish] generating consensus [=================> ] 0.201059 s\r[racon::Polisher::polish] generating consensus [==================> ] 0.201098 s\r[racon::Polisher::polish] generating consensus [===================>] 0.223171 s\r[racon::Polisher::polish] generating consensus [====================] 0.279729 s\n[racon::Polisher::] total = 0.455997 s\n", "job_stdout": "", "job_stderr": "", "stderr": "[racon::Polisher::initialize] loaded target sequences 0.001212 s\n[racon::Polisher::initialize] loaded sequences 0.015353 s\n[racon::Polisher::initialize] loaded overlaps 0.000635 s\n[racon::Polisher::initialize] aligning overlaps [=> ] 0.023210 s\r[racon::Polisher::initialize] aligning overlaps [==> ] 0.033253 s\r[racon::Polisher::initialize] aligning overlaps [===> ] 0.034746 s\r[racon::Polisher::initialize] aligning overlaps [====> ] 0.037507 s\r[racon::Polisher::initialize] aligning overlaps [=====> ] 0.056783 s\r[racon::Polisher::initialize] aligning overlaps [======> ] 0.056866 s\r[racon::Polisher::initialize] aligning overlaps [=======> ] 0.059320 s\r[racon::Polisher::initialize] aligning overlaps [========> ] 0.067356 s\r[racon::Polisher::initialize] aligning overlaps [=========> ] 0.079894 s\r[racon::Polisher::initialize] aligning overlaps [==========> ] 0.082588 s\r[racon::Polisher::initialize] aligning overlaps [===========> ] 0.086414 s\r[racon::Polisher::initialize] aligning overlaps [============> ] 0.092322 s\r[racon::Polisher::initialize] aligning overlaps [=============> ] 0.105871 s\r[racon::Polisher::initialize] aligning overlaps [==============> ] 0.106335 s\r[racon::Polisher::initialize] aligning overlaps [===============> ] 0.116799 s\r[racon::Polisher::initialize] aligning overlaps [================> ] 0.128586 s\r[racon::Polisher::initialize] aligning overlaps [=================> ] 0.128676 s\r[racon::Polisher::initialize] aligning overlaps [==================> ] 0.134370 s\r[racon::Polisher::initialize] aligning overlaps [===================>] 0.137779 s\r[racon::Polisher::initialize] aligning overlaps [====================] 0.156020 s\n[racon::Polisher::initialize] transformed data into windows 0.000433 s\n[racon::Polisher::polish] generating consensus [=> ] 0.027790 s\r[racon::Polisher::polish] generating consensus [==> ] 0.027881 s\r[racon::Polisher::polish] generating consensus [===> ] 0.042281 s\r[racon::Polisher::polish] generating consensus [====> ] 0.042387 s\r[racon::Polisher::polish] generating consensus [=====> ] 0.049526 s\r[racon::Polisher::polish] generating consensus [======> ] 0.051153 s\r[racon::Polisher::polish] generating consensus [=======> ] 0.057800 s\r[racon::Polisher::polish] generating consensus [========> ] 0.061971 s\r[racon::Polisher::polish] generating consensus [=========> ] 0.069788 s\r[racon::Polisher::polish] generating consensus [==========> ] 0.082611 s\r[racon::Polisher::polish] generating consensus [===========> ] 0.103810 s\r[racon::Polisher::polish] generating consensus [============> ] 0.110494 s\r[racon::Polisher::polish] generating consensus [=============> ] 0.144806 s\r[racon::Polisher::polish] generating consensus [==============> ] 0.151725 s\r[racon::Polisher::polish] generating consensus [===============> ] 0.176979 s\r[racon::Polisher::polish] generating consensus [================> ] 0.179273 s\r[racon::Polisher::polish] generating consensus [=================> ] 0.201059 s\r[racon::Polisher::polish] generating consensus [==================> ] 0.201098 s\r[racon::Polisher::polish] generating consensus [===================>] 0.223171 s\r[racon::Polisher::polish] generating consensus [====================] 0.279729 s\n[racon::Polisher::] total = 0.455997 s\n", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 18:34:08", "plugin": "core", "name": "end_epoch", "raw_value": "1698172448.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:34:08", "plugin": "core", "name": "start_epoch", "raw_value": "1698172448.0000000"}, {"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/2.0.4-0", "has_data": true, "data": {"tool_id": "samtools_idxstats", "tool_version": "2.0.4", "test_index": 0, "time_seconds": 35.71216058731079, "inputs": {"input": {"src": "hda", "id": "998e2a92f2ccacfb"}}, "job": {"model_class": "Job", "id": "4616f9c9a59bf3e9", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:57:11.084009", "create_time": "2023-10-24T18:56:53.963980", "galaxy_version": "23.1", "command_version": "Version: 1.13 (using htslib 1.13)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4", "history_id": "ac0b688889bc6865", "external_id": "gxy-96s4q", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/f/7/4/dataset_f74d5b1a-d68e-4e2e-b028-709edd0f7c33.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/0/a/7/metadata_0a73d2b8-30d7-42ac-99e8-07f6f1fbe269.dat' infile.bai && samtools idxstats -@ $addthreads infile > '/galaxy/server/database/objects/c/d/c/dataset_cdc95daf-d37e-4e7e-a061-434a2bcfe6a1.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input": {"id": "998e2a92f2ccacfb", "src": "hda", "uuid": "f74d5b1a-d68e-4e2e-b028-709edd0f7c33"}}, "outputs": {"output": {"id": "073a0278eb9c49f1", "src": "hda", "uuid": "cdc95daf-d37e-4e7e-a061-434a2bcfe6a1"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 18:56:59", "plugin": "core", "name": "end_epoch", "raw_value": "1698173819.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:56:59", "plugin": "core", "name": "start_epoch", "raw_value": "1698173819.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_idxstats/2.0.4-0", "has_data": true, "data": {"tool_id": "samtools_idxstats", "tool_version": "2.0.4", "test_index": 0, "time_seconds": 31.441080570220947, "inputs": {"input": {"src": "hda", "id": "0c1e1da0ee90ca11"}}, "job": {"model_class": "Job", "id": "bd04633f9b0feeef", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:58:16.716057", "create_time": "2023-10-24T18:58:05.181836", "galaxy_version": "23.1", "command_version": "Version: 1.13 (using htslib 1.13)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4", "history_id": "ac0b688889bc6865", "external_id": "gxy-jhfgs", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/b/c/a/dataset_bca93252-cab9-439c-888a-dd6803fcef27.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/c/e/0/metadata_ce07832e-df3b-4cb6-8545-f002d71e1f1a.dat' infile.bai && samtools idxstats -@ $addthreads infile > '/galaxy/server/database/objects/9/f/0/dataset_9f0cc581-ca05-4e3c-b93a-c71749937dc6.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input": {"id": "0c1e1da0ee90ca11", "src": "hda", "uuid": "bca93252-cab9-439c-888a-dd6803fcef27"}}, "outputs": {"output": {"id": "d31065b150c6a316", "src": "hda", "uuid": "9f0cc581-ca05-4e3c-b93a-c71749937dc6"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 18:58:07", "plugin": "core", "name": "end_epoch", "raw_value": "1698173887.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:58:07", "plugin": "core", "name": "start_epoch", "raw_value": "1698173887.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_idxstats/2.0.4-1", "has_data": true, "data": {"tool_id": "samtools_idxstats", "tool_version": "2.0.4", "test_index": 1, "time_seconds": 32.39071726799011, "inputs": {"input": {"src": "hda", "id": "df0263d1bf00a252"}}, "job": {"model_class": "Job", "id": "0ba283993e024ac9", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:57:43.270449", "create_time": "2023-10-24T18:57:30.731837", "galaxy_version": "23.1", "command_version": "Version: 1.13 (using htslib 1.13)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4", "history_id": "ac0b688889bc6865", "external_id": "gxy-qhlz2", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/5/4/3/dataset_543b3b5c-6270-4ce3-b596-f581147a0515.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/a/8/6/metadata_a863ecfb-aa3b-4a02-ac86-d53564ec8ecb.dat' infile.bai && samtools idxstats -@ $addthreads infile > '/galaxy/server/database/objects/2/b/e/dataset_2bed15a6-6ec3-43ab-954b-0f76ea7e4923.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input": {"id": "df0263d1bf00a252", "src": "hda", "uuid": "543b3b5c-6270-4ce3-b596-f581147a0515"}}, "outputs": {"output": {"id": "3e76028fc67617e9", "src": "hda", "uuid": "2bed15a6-6ec3-43ab-954b-0f76ea7e4923"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 18:57:33", "plugin": "core", "name": "end_epoch", "raw_value": "1698173853.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:57:33", "plugin": "core", "name": "start_epoch", "raw_value": "1698173853.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_idxstats/2.0.4-1", "has_data": true, "data": {"tool_id": "samtools_idxstats", "tool_version": "2.0.4", "test_index": 1, "time_seconds": 31.469481229782104, "inputs": {"input": {"src": "hda", "id": "eaaa83d05f1c427c"}}, "job": {"model_class": "Job", "id": "3155a4b1859c18a6", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T18:58:48.304207", "create_time": "2023-10-24T18:58:36.359282", "galaxy_version": "23.1", "command_version": "Version: 1.13 (using htslib 1.13)", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4", "history_id": "ac0b688889bc6865", "external_id": "gxy-bx626", "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/e/4/2/dataset_e42411d8-85dd-4671-a41b-3804f88f8579.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/1/e/9/metadata_1e9fd411-816c-4341-894f-0ebaf259a812.dat' infile.bai && samtools idxstats -@ $addthreads infile > '/galaxy/server/database/objects/b/3/2/dataset_b32c58ff-083f-44f0-8bed-18f97252f2be.dat'", "traceback": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input": {"id": "eaaa83d05f1c427c", "src": "hda", "uuid": "e42411d8-85dd-4671-a41b-3804f88f8579"}}, "outputs": {"output": {"id": "33095ef16140ba3b", "src": "hda", "uuid": "b32c58ff-083f-44f0-8bed-18f97252f2be"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 18:58:38", "plugin": "core", "name": "end_epoch", "raw_value": "1698173918.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 18:58:38", "plugin": "core", "name": "start_epoch", "raw_value": "1698173918.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter_cells/1.8.1+3+galaxy0-0", "has_data": true, "data": {"tool_id": "scanpy_filter_cells", "tool_version": "1.8.1+3+galaxy0", "test_index": 0, "time_seconds": 0.30519962310791016, "execution_problem": "Input staging problem: Test input file (read_10x.h5) cannot be found.", "status": "error"}}, {"id": "scanpy_filter_cells/1.8.1+3+galaxy0-0", "has_data": true, "data": {"tool_id": "scanpy_filter_cells", "tool_version": "1.8.1+3+galaxy0", "test_index": 0, "time_seconds": 0.29259252548217773, "execution_problem": "Input staging problem: Test input file (read_10x.h5) cannot be found.", "status": "error"}}, {"id": "scater_plot_pca/1.22.0-0", "has_data": true, "data": {"tool_id": "scater_plot_pca", "tool_version": "1.22.0", "test_index": 0, "time_seconds": 11.855453252792358, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "scater_plot_pca/1.22.0-0", "has_data": true, "data": {"tool_id": "scater_plot_pca", "tool_version": "1.22.0", "test_index": 0, "time_seconds": 73.50125098228455, "inputs": {"input_loom": {"src": "hda", "id": "9d67047ce9b8d6ff"}, "colour_by": "Treatment", "shape_by": "Mutation_Status"}, "job": {"model_class": "Job", "id": "d5b0c18913f66bf3", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:12:20.800821", "create_time": "2023-10-24T19:11:27.411694", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.22.0", "history_id": "ac0b688889bc6865", "external_id": "gxy-zm649", "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/e/e/b/dataset_eeb32179-b3c9-40c6-86e2-937ebfb843a1.dat' --colour-by 'Treatment' --shape-by 'Mutation_Status' -o '/galaxy/server/database/objects/8/5/b/dataset_85be8881-59d7-4f07-883b-0f47c14c9daa.dat'", "traceback": null, "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": "9d67047ce9b8d6ff", "src": "hda", "uuid": "eeb32179-b3c9-40c6-86e2-937ebfb843a1"}}, "outputs": {"output_plot": {"id": "0a5682db3809ca9d", "src": "hda", "uuid": "85be8881-59d7-4f07-883b-0f47c14c9daa"}}, "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, 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_stdout": "", "job_stderr": "", "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", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "11 seconds", "plugin": 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"2023-10-24T19:13:28.301039", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-2bh7n", "command_line": "ln -f -s '/galaxy/server/database/objects/1/4/1/dataset_141c1d08-0e01-4cbb-9023-a12ec955f6b7.dat' input.bam && ln -f -s '/galaxy/server/database/objects/_metadata_files/0/8/2/metadata_0824e63a-1c41-48e7-a287-0eedfe95b273.dat' input.bam.bai && sniffles -t ${GALAXY_SLOTS:-2} -m 'input.bam' -v '/galaxy/server/database/objects/a/8/2/dataset_a82c5b24-4ba5-47a2-b8de-6dbe24e09913.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", "traceback": null, "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": "1ca8b55c6d9ac19d", "src": "hda", "uuid": "141c1d08-0e01-4cbb-9023-a12ec955f6b7"}}, "outputs": {"output": {"id": "893bbd7cde8ce7c0", "src": "hda", "uuid": "a82c5b24-4ba5-47a2-b8de-6dbe24e09913"}}, "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": "", "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", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 19:13:33", "plugin": "core", "name": "end_epoch", "raw_value": "1698174813.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:13:33", "plugin": "core", "name": "start_epoch", "raw_value": "1698174813.0000000"}, {"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": 33.38603138923645, "inputs": {"input": {"src": "hda", "id": "eab6688cf88d7694"}, "general_options|num_reads_report": "-1"}, "job": {"model_class": "Job", "id": "767deaf2439ef47a", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:14:18.416200", "create_time": "2023-10-24T19:14:05.718207", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-q7rx7", "command_line": "ln -f -s '/galaxy/server/database/objects/f/9/0/dataset_f907272e-89fc-4ef7-ab2e-8190dcde3f8d.dat' input.bam && ln -f -s '/galaxy/server/database/objects/_metadata_files/f/a/2/metadata_fa21f7bd-bf2d-47d0-aa7f-5d2e0ec457e5.dat' input.bam.bai && sniffles -t ${GALAXY_SLOTS:-2} -m 'input.bam' -v '/galaxy/server/database/objects/a/c/d/dataset_acd2ac21-e70b-493c-8cb6-9dc8d34de0fb.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", "traceback": null, "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": "eab6688cf88d7694", "src": "hda", "uuid": "f907272e-89fc-4ef7-ab2e-8190dcde3f8d"}}, "outputs": {"output": {"id": "9343a8ecb26c3c3e", "src": "hda", "uuid": "acd2ac21-e70b-493c-8cb6-9dc8d34de0fb"}}, "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": "", "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", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 19:14:07", "plugin": "core", "name": "end_epoch", "raw_value": "1698174847.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:14:07", "plugin": "core", "name": "start_epoch", "raw_value": "1698174847.0000000"}, {"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": 31.149372100830078, "inputs": {"input": {"src": "hda", "id": "062c633ce2d00f23"}, "general_options|cs_string": true}, "job": {"model_class": "Job", "id": "b1011fcf88d7c815", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:14:49.806020", "create_time": "2023-10-24T19:14:38.284178", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-24rfs", "command_line": "ln -f -s '/galaxy/server/database/objects/0/a/6/dataset_0a6c53bf-4585-410e-9988-e0ee53317909.dat' input.bam && ln -f -s '/galaxy/server/database/objects/_metadata_files/f/9/3/metadata_f93cb4e5-0dd9-45c8-ad5f-14f49af57715.dat' input.bam.bai && sniffles -t ${GALAXY_SLOTS:-2} -m 'input.bam' -v '/galaxy/server/database/objects/b/3/2/dataset_b32eb93d-45ae-4afa-bd31-719067f1d620.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", "traceback": null, "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": "062c633ce2d00f23", "src": "hda", "uuid": "0a6c53bf-4585-410e-9988-e0ee53317909"}}, "outputs": {"output": {"id": "2690ce60900b8d77", "src": "hda", "uuid": "b32eb93d-45ae-4afa-bd31-719067f1d620"}}, "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": "", "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", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 19:14:39", "plugin": "core", "name": "end_epoch", "raw_value": "1698174879.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:14:39", "plugin": "core", "name": "start_epoch", "raw_value": "1698174879.0000000"}, {"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": 33.369778633117676, "inputs": {"input": {"src": "hda", "id": "e7ea7b7bd60f81ff"}, "clustering_options|cluster": true}, "job": {"model_class": "Job", "id": "da7389a04184544d", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:15:23.117304", "create_time": "2023-10-24T19:15:10.529010", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-h628f", "command_line": "ln -f -s '/galaxy/server/database/objects/0/8/3/dataset_08341ab6-cb6e-4d60-acd0-d09ad7734815.dat' input.bam && ln -f -s '/galaxy/server/database/objects/_metadata_files/d/9/f/metadata_d9f983d4-9053-4fb2-b721-d9b76d4b6977.dat' input.bam.bai && sniffles -t ${GALAXY_SLOTS:-2} -m 'input.bam' -v '/galaxy/server/database/objects/5/f/b/dataset_5fb80b1d-d56b-4769-b9fb-e7207f64a824.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", "traceback": null, "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": "e7ea7b7bd60f81ff", "src": "hda", "uuid": "08341ab6-cb6e-4d60-acd0-d09ad7734815"}}, "outputs": {"output": {"id": "862337209f83c0c3", "src": "hda", "uuid": "5fb80b1d-d56b-4769-b9fb-e7207f64a824"}}, "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": "", "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", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 19:15:12", "plugin": "core", "name": "end_epoch", "raw_value": "1698174912.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:15:12", "plugin": "core", "name": "start_epoch", "raw_value": "1698174912.0000000"}, {"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": 32.04981970787048, "inputs": {"input": {"src": "hda", "id": "0b8b5ed89fd0f60a"}, "advanced_options|report_BND": true}, "job": {"model_class": "Job", "id": "06d7fb44a508cab8", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:15:55.596538", "create_time": "2023-10-24T19:15:43.991968", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-gb4jx", "command_line": "ln -f -s '/galaxy/server/database/objects/b/c/e/dataset_bceb9629-19bd-4ee7-854c-fb4719b60d3a.dat' input.bam && ln -f -s '/galaxy/server/database/objects/_metadata_files/e/4/e/metadata_e4e2910d-ac8f-44a2-93ee-06ae3fde5f20.dat' input.bam.bai && sniffles -t ${GALAXY_SLOTS:-2} -m 'input.bam' -v '/galaxy/server/database/objects/7/1/c/dataset_71c9188e-dfcd-49f7-a1ad-ad7d4abba031.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", "traceback": null, "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": "0b8b5ed89fd0f60a", "src": "hda", "uuid": "bceb9629-19bd-4ee7-854c-fb4719b60d3a"}}, "outputs": {"output": {"id": "f2bddb634099cedc", "src": "hda", "uuid": "71c9188e-dfcd-49f7-a1ad-ad7d4abba031"}}, "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": "", "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", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 19:15:45", "plugin": "core", "name": "end_epoch", "raw_value": "1698174945.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:15:45", "plugin": "core", "name": "start_epoch", "raw_value": "1698174945.0000000"}, {"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": 32.504801511764526, "inputs": {"input": {"src": "hda", "id": "39bc59f2bc6a7d83"}, "parameter_estimation_options|skip_parameter_estimation": true}, "job": {"model_class": "Job", "id": "c8f9a407456ea49a", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:16:28.142590", "create_time": "2023-10-24T19:16:16.172981", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-kwfmd", "command_line": "ln -f -s '/galaxy/server/database/objects/a/d/c/dataset_adc4bfe1-f992-400d-b58f-fd10e0d68385.dat' input.bam && ln -f -s '/galaxy/server/database/objects/_metadata_files/1/e/1/metadata_1e1a49ef-50b2-40a1-85d3-f1fb0d453192.dat' input.bam.bai && sniffles -t ${GALAXY_SLOTS:-2} -m 'input.bam' -v '/galaxy/server/database/objects/c/f/4/dataset_cf4fce29-0e1f-4bad-8df3-f361c9a56c55.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", "traceback": null, "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": "39bc59f2bc6a7d83", "src": "hda", "uuid": "adc4bfe1-f992-400d-b58f-fd10e0d68385"}}, "outputs": {"output": {"id": "a889b988f198ada4", "src": "hda", "uuid": "cf4fce29-0e1f-4bad-8df3-f361c9a56c55"}}, "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": "", "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", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 19:16:17", "plugin": "core", "name": "end_epoch", "raw_value": "1698174977.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:16:17", "plugin": "core", "name": "start_epoch", "raw_value": "1698174977.0000000"}, {"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": 38.77441191673279, "inputs": {"input1": {"src": "hda", "id": "5d7ffaad759a0358"}}, "job": {"model_class": "Job", "id": "062c633ce2d00f23", "state": "ok", "exit_code": 0, "update_time": "2023-10-24T19:23:50.205313", "create_time": "2023-10-24T19:23:30.522789", "galaxy_version": "23.1", "command_version": "", "copied_from_job_id": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0", "history_id": "ac0b688889bc6865", "external_id": "gxy-w5d7q", "command_line": "vcffixup '/galaxy/server/database/objects/d/8/d/dataset_d8d896de-2011-4428-8e18-f5a2444cc854.dat' > '/galaxy/server/database/objects/d/1/6/dataset_d16a4774-402d-4796-bdda-7140436c10a3.dat'", "traceback": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input1": {"id": "5d7ffaad759a0358", "src": "hda", "uuid": "d8d896de-2011-4428-8e18-f5a2444cc854"}}, "outputs": {"out_file1": {"id": "c530f1cf6f236d12", "src": "hda", "uuid": "d16a4774-402d-4796-bdda-7140436c10a3"}}, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stderr": "", "stdout": "", "job_messages": [], "dependencies": [], "user_email": "tests@fake.org", "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2023-10-24 19:23:38", "plugin": "core", "name": "end_epoch", "raw_value": "1698175418.0000000"}, {"title": "Job Start Time", "value": "2023-10-24 19:23:38", "plugin": "core", "name": "start_epoch", "raw_value": "1698175418.0000000"}, {"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": "vcftools_annotate/0.1-0", "has_data": true, "data": {"tool_id": "vcftools_annotate", "tool_version": "0.1", "test_index": 0, "time_seconds": 12.005725622177124, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}], "galaxy_url": "http://34.23.248.223:8000/galaxy/"} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/results.xunit b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/results.xunit new file mode 100644 index 000000000..1b9c7f9eb --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/results.xunit @@ -0,0 +1,1064 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + sys.exit(main()) File "/usr/local/lib/python3.8/site-packages/ncbi_acc_download/__main__.py", line 54, in main download_to_file(dl_id, config, filename, append) File "/usr/local/lib/python3.8/site-packages/ncbi_acc_download/core.py", line 110, in download_to_file r = get_stream(url, params) File "/usr/local/lib/python3.8/site-packages/ncbi_acc_download/download.py", line 90, in get_stream raise DownloadError("Download failed with return code: {}".format(r.status_code))ncbi_acc_download.errors.DownloadError: Download failed with return code: 400 + ]]> + + + + + + + + sys.exit(main()) File "/usr/local/lib/python3.8/site-packages/ncbi_acc_download/__main__.py", line 54, in main download_to_file(dl_id, config, filename, append) File "/usr/local/lib/python3.8/site-packages/ncbi_acc_download/core.py", line 110, in download_to_file r = get_stream(url, params) File "/usr/local/lib/python3.8/site-packages/ncbi_acc_download/download.py", line 90, in get_stream raise DownloadError("Download failed with return code: {}".format(r.status_code))ncbi_acc_download.errors.DownloadError: Download failed with return code: 400 + ]]> + + + + + + + + sys.exit(main()) File "/usr/local/lib/python3.8/site-packages/ncbi_acc_download/__main__.py", line 54, in main download_to_file(dl_id, config, filename, append) File "/usr/local/lib/python3.8/site-packages/ncbi_acc_download/core.py", line 110, in download_to_file r = get_stream(url, params) File "/usr/local/lib/python3.8/site-packages/ncbi_acc_download/download.py", line 90, in get_stream raise DownloadError("Download failed with return code: {}".format(r.status_code))ncbi_acc_download.errors.DownloadError: Download failed with return code: 400 + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ] 0.003563 s[racon::Polisher::initialize] aligning overlaps [==> ] 0.003584 s[racon::Polisher::initialize] aligning overlaps [===> ] 0.003688 s[racon::Polisher::initialize] aligning overlaps [====> ] 0.005533 s[racon::Polisher::initialize] aligning overlaps [=====> ] 0.005550 s[racon::Polisher::initialize] aligning overlaps [======> ] 0.005560 s[racon::Polisher::initialize] aligning overlaps [=======> ] 0.005570 s[racon::Polisher::initialize] aligning overlaps [========> ] 0.005581 s[racon::Polisher::initialize] aligning overlaps [=========> ] 0.005591 s[racon::Polisher::initialize] aligning overlaps [==========> ] 0.005602 s[racon::Polisher::initialize] aligning overlaps [===========> ] 0.005612 s[racon::Polisher::initialize] aligning overlaps [============> ] 0.005622 s[racon::Polisher::initialize] aligning overlaps [=============> ] 0.005632 s[racon::Polisher::initialize] aligning overlaps [==============> ] 0.005643 s[racon::Polisher::initialize] aligning overlaps [===============> ] 0.005653 s[racon::Polisher::initialize] aligning overlaps [================> ] 0.005663 s[racon::Polisher::initialize] aligning overlaps [=================> ] 0.005674 s[racon::Polisher::initialize] aligning overlaps [==================> ] 0.005684 s[racon::Polisher::initialize] aligning overlaps [===================>] 0.005695 s[racon::Polisher::initialize] aligning overlaps [====================] 0.005705 s[racon::Polisher::initialize] transformed data into windows 0.000330 s[racon::Polisher::polish] generating consensus [=> ] 0.099324 s[racon::Polisher::polish] generating consensus [==> ] 0.099368 s[racon::Polisher::polish] generating consensus [===> ] 0.099397 s[racon::Polisher::polish] generating consensus [====> ] 0.101504 s[racon::Polisher::polish] generating consensus [=====> ] 0.105243 s[racon::Polisher::polish] generating consensus [======> ] 0.125058 s[racon::Polisher::polish] generating consensus [=======> ] 0.140161 s[racon::Polisher::polish] generating consensus [========> ] 0.174749 s[racon::Polisher::polish] generating consensus [=========> ] 0.213913 s[racon::Polisher::polish] generating consensus [==========> ] 0.238018 s[racon::Polisher::polish] generating consensus [===========> ] 0.316152 s[racon::Polisher::polish] generating consensus [============> ] 0.316945 s[racon::Polisher::polish] generating consensus [=============> ] 0.350444 s[racon::Polisher::polish] generating consensus [==============> ] 0.392238 s[racon::Polisher::polish] generating consensus [===============> ] 0.392391 s[racon::Polisher::polish] generating consensus [================> ] 0.443380 s[racon::Polisher::polish] generating consensus [=================> ] 0.443424 s[racon::Polisher::polish] generating consensus [==================> ] 0.467153 s[racon::Polisher::polish] generating consensus [===================>] 0.493275 s[racon::Polisher::polish] generating consensus [====================] 0.509450 s[racon::Polisher::] total = 0.546181 s + ]]> + + + + + + + + ] 0.023210 s[racon::Polisher::initialize] aligning overlaps [==> ] 0.033253 s[racon::Polisher::initialize] aligning overlaps [===> ] 0.034746 s[racon::Polisher::initialize] aligning overlaps [====> ] 0.037507 s[racon::Polisher::initialize] aligning overlaps [=====> ] 0.056783 s[racon::Polisher::initialize] aligning overlaps [======> ] 0.056866 s[racon::Polisher::initialize] aligning overlaps [=======> ] 0.059320 s[racon::Polisher::initialize] aligning overlaps [========> ] 0.067356 s[racon::Polisher::initialize] aligning overlaps [=========> ] 0.079894 s[racon::Polisher::initialize] aligning overlaps [==========> ] 0.082588 s[racon::Polisher::initialize] aligning overlaps [===========> ] 0.086414 s[racon::Polisher::initialize] aligning overlaps [============> ] 0.092322 s[racon::Polisher::initialize] aligning overlaps [=============> ] 0.105871 s[racon::Polisher::initialize] aligning overlaps [==============> ] 0.106335 s[racon::Polisher::initialize] aligning overlaps [===============> ] 0.116799 s[racon::Polisher::initialize] aligning overlaps [================> ] 0.128586 s[racon::Polisher::initialize] aligning overlaps [=================> ] 0.128676 s[racon::Polisher::initialize] aligning overlaps [==================> ] 0.134370 s[racon::Polisher::initialize] aligning overlaps [===================>] 0.137779 s[racon::Polisher::initialize] aligning overlaps [====================] 0.156020 s[racon::Polisher::initialize] transformed data into windows 0.000433 s[racon::Polisher::polish] generating consensus [=> ] 0.027790 s[racon::Polisher::polish] generating consensus [==> ] 0.027881 s[racon::Polisher::polish] generating consensus [===> ] 0.042281 s[racon::Polisher::polish] generating consensus [====> ] 0.042387 s[racon::Polisher::polish] generating consensus [=====> ] 0.049526 s[racon::Polisher::polish] generating consensus [======> ] 0.051153 s[racon::Polisher::polish] generating consensus [=======> ] 0.057800 s[racon::Polisher::polish] generating consensus [========> ] 0.061971 s[racon::Polisher::polish] generating consensus [=========> ] 0.069788 s[racon::Polisher::polish] generating consensus [==========> ] 0.082611 s[racon::Polisher::polish] generating consensus [===========> ] 0.103810 s[racon::Polisher::polish] generating consensus [============> ] 0.110494 s[racon::Polisher::polish] generating consensus [=============> ] 0.144806 s[racon::Polisher::polish] generating consensus [==============> ] 0.151725 s[racon::Polisher::polish] generating consensus [===============> ] 0.176979 s[racon::Polisher::polish] generating consensus [================> ] 0.179273 s[racon::Polisher::polish] generating consensus [=================> ] 0.201059 s[racon::Polisher::polish] generating consensus [==================> ] 0.201098 s[racon::Polisher::polish] generating consensus [===================>] 0.223171 s[racon::Polisher::polish] generating consensus [====================] 0.279729 s[racon::Polisher::] total = 0.455997 s + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/tools.yml b/reports/anvil-edge/tool-tests/edge-23-10-24-18-13-1/tools.yml new file mode 100644 index 000000000..96c903b6a --- /dev/null +++ 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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: vcffixup + owner: devteam + revisions: + - 11f62f071125 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: vcftools_annotate + owner: devteam + revisions: + - 57a6550df582 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF