From 73d533ff5acc9ad8c29b1c255f57e8924343f28c Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Wed, 4 Sep 2024 19:33:59 +0000 Subject: [PATCH] Updating anvil-edge README for edge-24-09-04-18-15-1 --- reports/anvil-edge/README.md | 2 +- reports/anvil-edge/tool-tests/chunks.json | 10 +- .../edge-24-09-04-18-15-1/chunk.json | 7 + .../edge-24-09-04-18-15-1/chunk.txt | 25 + .../errors/041a65779e107113.json | 45 + .../errors/09976a7dbbbe05e4.json | 45 + .../errors/0a3d65af2197e1a0.json | 45 + .../errors/0a3ea1b885987c08.json | 54 + .../errors/25718ce0aef57e36.json | 69 ++ .../errors/36df2befc514ba6e.json | 45 + .../errors/36fea06678d221ff.json | 52 + .../errors/4ce9828a66d14df3.json | 45 + .../errors/6cb2c6ca63395177.json | 45 + .../errors/c676976b61076d41.json | 45 + .../errors/ca8200a9c07f5244.json | 45 + .../errors/ce798158709471b6.json | 45 + .../errors/d3dd358c0a8193fa.json | 45 + .../errors/efdc907f4a8e4544.json | 67 ++ .../errors/f263adfadf1d211f.json | 45 + .../edge-24-09-04-18-15-1/job-metrics.csv | 206 ++++ .../tool-tests/edge-24-09-04-18-15-1/jobs.txt | 205 ++++ .../edge-24-09-04-18-15-1/results.html | 291 ++++++ .../edge-24-09-04-18-15-1/results.json | 1 + .../edge-24-09-04-18-15-1/results.xunit | 972 ++++++++++++++++++ .../edge-24-09-04-18-15-1/tools.yml | 127 +++ 25 files changed, 2577 insertions(+), 6 deletions(-) create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/chunk.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/chunk.txt create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/041a65779e107113.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/09976a7dbbbe05e4.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/0a3d65af2197e1a0.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/0a3ea1b885987c08.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/25718ce0aef57e36.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/36df2befc514ba6e.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/36fea06678d221ff.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/4ce9828a66d14df3.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/6cb2c6ca63395177.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/c676976b61076d41.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/ca8200a9c07f5244.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/ce798158709471b6.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/d3dd358c0a8193fa.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/efdc907f4a8e4544.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/f263adfadf1d211f.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/job-metrics.csv create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/jobs.txt create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/results.html create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/results.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/results.xunit create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/tools.yml diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md index 7a35b5de8..dcfadb645 100644 --- a/reports/anvil-edge/README.md +++ b/reports/anvil-edge/README.md @@ -13,4 +13,4 @@ After each successful deployment, automated tool tests are also run against the Latest tool tests for each chunk: -
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 02 06:26:43 2024Mon Aug 26 06:26:05 2024
1ToolsetMon Sep 02 18:31:49 2024Mon Aug 26 18:31:46 2024
2ToolsetTue Sep 03 06:25:36 2024Tue Aug 27 06:26:39 2024
3ToolsetTue Sep 03 18:31:25 2024Tue Aug 27 18:39:36 2024
4ToolsetWed Aug 28 06:26:28 2024Wed Aug 21 06:25:47 2024
5ToolsetWed Aug 21 18:31:30 2024Wed Aug 14 18:31:52 2024
6ToolsetThu Aug 29 06:25:45 2024Thu Aug 22 06:25:48 2024
7ToolsetThu Aug 29 18:32:00 2024Thu Aug 22 18:43:08 2024
8ToolsetFri Aug 30 06:25:36 2024Fri Aug 23 06:25:56 2024
9ToolsetFri Aug 30 18:31:41 2024Fri Aug 23 18:38:12 2024
10ToolsetSat Aug 31 06:24:40 2024Sat Aug 24 06:23:31 2024
11ToolsetSat Aug 31 18:29:37 2024Sat Aug 24 18:29:36 2024
12ToolsetSun Sep 01 06:26:20 2024Sun Aug 25 06:24:42 2024
13ToolsetSun Sep 01 18:29:57 2024Sun Aug 25 18:29:56 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 02 06:26:43 2024Mon Aug 26 06:26:05 2024
1ToolsetMon Sep 02 18:31:49 2024Mon Aug 26 18:31:46 2024
2ToolsetTue Sep 03 06:25:36 2024Tue Aug 27 06:26:39 2024
3ToolsetTue Sep 03 18:31:25 2024Tue Aug 27 18:39:36 2024
4ToolsetWed Aug 28 06:26:28 2024Wed Aug 21 06:25:47 2024
5ToolsetWed Sep 04 18:30:27 2024Wed Aug 21 18:31:30 2024
6ToolsetThu Aug 29 06:25:45 2024Thu Aug 22 06:25:48 2024
7ToolsetThu Aug 29 18:32:00 2024Thu Aug 22 18:43:08 2024
8ToolsetFri Aug 30 06:25:36 2024Fri Aug 23 06:25:56 2024
9ToolsetFri Aug 30 18:31:41 2024Fri Aug 23 18:38:12 2024
10ToolsetSat Aug 31 06:24:40 2024Sat Aug 24 06:23:31 2024
11ToolsetSat Aug 31 18:29:37 2024Sat Aug 24 18:29:36 2024
12ToolsetSun Sep 01 06:26:20 2024Sun Aug 25 06:24:42 2024
13ToolsetSun Sep 01 18:29:57 2024Sun Aug 25 18:29:56 2024
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json index 933a2f425..4b92fb001 100644 --- a/reports/anvil-edge/tool-tests/chunks.json +++ b/reports/anvil-edge/tool-tests/chunks.json @@ -28,11 +28,11 @@ "date2": "Wed Aug 21 06:25:47 2024" }, "5": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-21-18-16-1/results.html", - "date1": "Wed Aug 21 18:31:30 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-21-18-16-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-14-18-15-1/results.html", - "date2": "Wed Aug 14 18:31:52 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/results.html", + "date1": "Wed Sep 04 18:30:27 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-21-18-16-1/results.html", + "date2": "Wed Aug 21 18:31:30 2024" }, "6": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-29-06-11-1/results.html", diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/chunk.json new file mode 100644 index 000000000..4f27ce33f --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/chunk.json @@ -0,0 +1,7 @@ +{ + "5": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/results.html", + "date1": "Wed Sep 04 18:30:27 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/chunk.txt new file mode 100644 index 000000000..b50e02586 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/chunk.txt @@ -0,0 +1,25 @@ +-t collapse_collections --tool-version 90981f86000f +-t deeptools_multi_bam_summary --tool-version 78f405266706 +-t fastq_paired_end_deinterlacer --tool-version f3936d0632cb +-t circos --tool-version df7356989ac1 +-t mummer_mummer --tool-version 48823c9635a4 +-t porechop --tool-version 93d623d9979c +-t limma_voom --tool-version 0921444c832d +-t limma_voom --tool-version d6f5fa4ee473 +-t sam2interval --tool-version 75557c0908a9 +-t samtools_flagstat --tool-version 22970df7a40e +-t music_construct_eset --tool-version 282819d09a4f +-t music_construct_eset --tool-version 2cfd0db49bbc +-t raceid_clustering --tool-version a4b734cd253b +-t raceid_clustering --tool-version f911a64454fb +-t scanpy_filter --tool-version b409c2486353 +-t scanpy_normalise_data --tool-version 439f7f939d46 +-t scanpy_normalise_data --tool-version 463d4fa8f5ec +-t annotatemyids --tool-version 44018dd6b447 +-t annotatemyids --tool-version fe3ca740a485 +-t diff --tool-version 156d0908e232 +-t bcftools_consensus --tool-version d6dc477167f8 +-t bcftools_plugin_impute_info --tool-version 776ad0b21536 +-t bcftools_query --tool-version c9c5718edc19 +-t vcfgeno2haplo --tool-version a3dea556218d +-t ivar_trim --tool-version db536ad45f28 diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/041a65779e107113.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/041a65779e107113.json new file mode 100644 index 000000000..a766834a2 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/041a65779e107113.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "041a65779e107113", + "history_id": "3cbec5b19229f469", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T18:44:20.942480", + "update_time": "2024-09-04T18:44:32.249013", + "galaxy_version": "24.1", + "external_id": "gxy-qzjfw", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/43/registry.xml' '/galaxy/server/database/jobs_directory/000/43/upload_params.json' '63:/galaxy/server/database/objects/a/7/b/dataset_a7b30079-21c9-45a3-8c69-6c7fd289d76b_files:/galaxy/server/database/objects/a/7/b/dataset_a7b30079-21c9-45a3-8c69-6c7fd289d76b.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_q3aevr1i\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"factorinfo.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_3u_pu91e\", \"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": "4bad1a2b93025157", + "src": "hda", + "uuid": "a7b30079-21c9-45a3-8c69-6c7fd289d76b" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/09976a7dbbbe05e4.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/09976a7dbbbe05e4.json new file mode 100644 index 000000000..e17d52b59 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/09976a7dbbbe05e4.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "09976a7dbbbe05e4", + "history_id": "3cbec5b19229f469", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T19:23:53.373692", + "update_time": "2024-09-04T19:24:03.542977", + "galaxy_version": "24.1", + "external_id": "gxy-5f2lr", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/163/registry.xml' '/galaxy/server/database/jobs_directory/000/163/upload_params.json' '245:/galaxy/server/database/objects/d/f/7/dataset_df78a9b9-6910-4c9e-839d-ff43b481a802_files:/galaxy/server/database/objects/d/f/7/dataset_df78a9b9-6910-4c9e-839d-ff43b481a802.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_osxn731w\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"file1.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_o3j_y0qq\", \"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": "061a6db00a48f33c", + "src": "hda", + "uuid": "df78a9b9-6910-4c9e-839d-ff43b481a802" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/0a3d65af2197e1a0.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/0a3d65af2197e1a0.json new file mode 100644 index 000000000..18215f738 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/0a3d65af2197e1a0.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "0a3d65af2197e1a0", + "history_id": "3cbec5b19229f469", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T19:24:41.130085", + "update_time": "2024-09-04T19:24:50.813497", + "galaxy_version": "24.1", + "external_id": "gxy-zc5zr", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/167/registry.xml' '/galaxy/server/database/jobs_directory/000/167/upload_params.json' '249:/galaxy/server/database/objects/a/2/a/dataset_a2a9b0f2-5655-4eb9-a9b4-56d732807c61_files:/galaxy/server/database/objects/a/2/a/dataset_a2a9b0f2-5655-4eb9-a9b4-56d732807c61.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_pq6mum_m\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"file1.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_b39zz2e0\", \"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": "8b09306c242ed41b", + "src": "hda", + "uuid": "a2a9b0f2-5655-4eb9-a9b4-56d732807c61" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/0a3ea1b885987c08.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/0a3ea1b885987c08.json new file mode 100644 index 000000000..7aa9795f6 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/0a3ea1b885987c08.json @@ -0,0 +1,54 @@ +{ + "model_class": "Job", + "id": "0a3ea1b885987c08", + "history_id": "3cbec5b19229f469", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T19:14:01.874664", + "update_time": "2024-09-04T19:14:10.613857", + "galaxy_version": "24.1", + "external_id": "gxy-cm9w5", + "handler": null, + "job_runner_name": null, + "command_line": "cp '/galaxy/server/database/objects/3/1/5/dataset_31560881-ef28-4f42-9279-93241afca87a.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/137/configs/tmpu5om38ov' > '/galaxy/server/database/objects/9/8/7/dataset_9871714f-f2ce-4a0f-bd7c-dba53bbd7541.dat' && python '/galaxy/server/database/jobs_directory/000/137/configs/tmpu5om38ov' >> '/galaxy/server/database/objects/9/8/7/dataset_9871714f-f2ce-4a0f-bd7c-dba53bbd7541.dat' && ls . >> '/galaxy/server/database/objects/9/8/7/dataset_9871714f-f2ce-4a0f-bd7c-dba53bbd7541.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "advanced_common": "{\"show_log\": true}", + "method": "{\"__current_case__\": 0, \"filter\": {\"__current_case__\": 3, \"filter\": \"max_genes\", \"max_genes\": \"100\"}, \"method\": \"pp.filter_cells\"}" + }, + "inputs": { + "adata": { + "id": "da8dabdc7a6c9084", + "src": "hda", + "uuid": "31560881-ef28-4f42-9279-93241afca87a" + } + }, + "outputs": { + "anndata_out": { + "id": "bec25e6b1a0850d8", + "src": "hda", + "uuid": "850fcd68-6380-4967-b7ab-508770596108" + }, + "hidden_output": { + "id": "ae6bb488985fa333", + "src": "hda", + "uuid": "9871714f-f2ce-4a0f-bd7c-dba53bbd7541" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n- n_genes\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", + "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n- n_genes\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", + "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/25718ce0aef57e36.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/25718ce0aef57e36.json new file mode 100644 index 000000000..3b57e92c5 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/25718ce0aef57e36.json @@ -0,0 +1,69 @@ +{ + "model_class": "Job", + "id": "25718ce0aef57e36", + "history_id": "3cbec5b19229f469", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T18:32:57.803959", + "update_time": "2024-09-04T18:33:03.041702", + "galaxy_version": "24.1", + "external_id": "gxy-gjv5d", + "handler": null, + "job_runner_name": null, + "command_line": "ln -s '/galaxy/server/database/objects/0/7/b/dataset_07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/2/6/4/metadata_2641dd70-609b-4f94-9c42-2b30489ecfa6.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/0/7/b/dataset_07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/2/6/4/metadata_2641dd70-609b-4f94-9c42-2b30489ecfa6.dat' './1.bam.bai' && multiBamSummary BED-file --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --outFileName '/galaxy/server/database/objects/5/f/5/dataset_5f516eee-0a8b-4a48-997f-5c7961be38d6.dat' --bamfiles '0.bam' '1.bam' --labels 'bowtie2 test1.bam' 'bowtie2 test1.bam' --BED /galaxy/server/database/objects/1/6/8/dataset_168b8377-1770-4dce-ba17-7aecf99d7738.dat", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"bam\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "scalingFactors": "false", + "outRawCounts": "false", + "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", + "region": "\"\"", + "mode": "{\"__current_case__\": 1, \"modeOpt\": \"BED-file\", \"region_file\": {\"values\": [{\"id\": 4, \"src\": \"hda\"}]}}", + "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", + "multibam_conditional": "{\"__current_case__\": 0, \"bamfiles\": {\"values\": [{\"id\": 3, \"src\": \"hda\"}, {\"id\": 3, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}" + }, + "inputs": { + "multibam_conditional|bamfiles": { + "id": "2e44e9ff029c6820", + "src": "hda", + "uuid": "07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9" + }, + "multibam_conditional|bamfiles1": { + "id": "2e44e9ff029c6820", + "src": "hda", + "uuid": "07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9" + }, + "multibam_conditional|bamfiles2": { + "id": "2e44e9ff029c6820", + "src": "hda", + "uuid": "07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9" + }, + "mode|region_file": { + "id": "7c84d18633e694f0", + "src": "hda", + "uuid": "168b8377-1770-4dce-ba17-7aecf99d7738" + } + }, + "outputs": { + "outFile": { + "id": "25718ce0aef57e36", + "src": "hda", + "uuid": "5f516eee-0a8b-4a48-997f-5c7961be38d6" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "Number of bins found: 3\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "Number of bins found: 3\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/36df2befc514ba6e.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/36df2befc514ba6e.json new file mode 100644 index 000000000..aa4c8b58a --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/36df2befc514ba6e.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "36df2befc514ba6e", + "history_id": "3cbec5b19229f469", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T18:59:31.848577", + "update_time": "2024-09-04T18:59:42.998921", + "galaxy_version": "24.1", + "external_id": "gxy-lpclb", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/106/registry.xml' '/galaxy/server/database/jobs_directory/000/106/upload_params.json' '153:/galaxy/server/database/objects/b/d/d/dataset_bdde608d-979e-40e8-a5aa-5d94e8e598a5_files:/galaxy/server/database/objects/b/d/d/dataset_bdde608d-979e-40e8-a5aa-5d94e8e598a5.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_3_kfdxpb\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"matrix.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_0yincmgu\", \"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": "ce798158709471b6", + "src": "hda", + "uuid": "bdde608d-979e-40e8-a5aa-5d94e8e598a5" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/36fea06678d221ff.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/36fea06678d221ff.json new file mode 100644 index 000000000..c3b24533b --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/36fea06678d221ff.json @@ -0,0 +1,52 @@ +{ + "model_class": "Job", + "id": "36fea06678d221ff", + "history_id": "3cbec5b19229f469", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T18:39:21.971793", + "update_time": "2024-09-04T18:39:26.733369", + "galaxy_version": "24.1", + "external_id": "gxy-fdq4b", + "handler": null, + "job_runner_name": null, + "command_line": "porechop -i '/galaxy/server/database/objects/8/d/5/dataset_8d57a286-02c8-46d6-8595-2feb13093603.dat' --format 'fasta.gz' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fasta.gz'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"fasta\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", + "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", + "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", + "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", + "format": "\"fasta.gz\"" + }, + "inputs": { + "input_file": { + "id": "f72f493266f70991", + "src": "hda", + "uuid": "8d57a286-02c8-46d6-8595-2feb13093603" + } + }, + "outputs": { + "outfile": { + "id": "4a3502ad1b1cd043", + "src": "hda", + "uuid": "adbc05b4-6865-4d52-8822-940affbbab7e" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/8/d/5/dataset_8d57a286-02c8-46d6-8595-2feb13093603.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 Short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR tail 1 63.3 63.3\n PCR tail 2 67.7 70.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\npigz not found - using gzip to compress\n\nSaved result to /galaxy/server/database/jobs_directory/000/28/working/out.fasta.gz\n\n", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/8/d/5/dataset_8d57a286-02c8-46d6-8595-2feb13093603.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 Short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR tail 1 63.3 63.3\n PCR tail 2 67.7 70.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\npigz not found - using gzip to compress\n\nSaved result to /galaxy/server/database/jobs_directory/000/28/working/out.fasta.gz\n\n", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/4ce9828a66d14df3.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/4ce9828a66d14df3.json new file mode 100644 index 000000000..7702b729c --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/4ce9828a66d14df3.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "4ce9828a66d14df3", + "history_id": "3cbec5b19229f469", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T19:15:28.767490", + "update_time": "2024-09-04T19:15:38.881060", + "galaxy_version": "24.1", + "external_id": "gxy-nwzxt", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/142/registry.xml' '/galaxy/server/database/jobs_directory/000/142/upload_params.json' '219:/galaxy/server/database/objects/d/5/b/dataset_d5bf364e-465e-4947-8305-5f23593e0e53_files:/galaxy/server/database/objects/d/5/b/dataset_d5bf364e-465e-4947-8305-5f23593e0e53.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_scie9orl\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"krumsiek11.h5ad\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_cdmqj50a\", \"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": "f3f69baaa2b32f52", + "src": "hda", + "uuid": "d5bf364e-465e-4947-8305-5f23593e0e53" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/6cb2c6ca63395177.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/6cb2c6ca63395177.json new file mode 100644 index 000000000..c4011b3f6 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/6cb2c6ca63395177.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "6cb2c6ca63395177", + "history_id": "3cbec5b19229f469", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T18:33:46.477446", + "update_time": "2024-09-04T18:33:56.634551", + "galaxy_version": "24.1", + "external_id": "gxy-n5rrz", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/8/registry.xml' '/galaxy/server/database/jobs_directory/000/8/upload_params.json' '11:/galaxy/server/database/objects/2/0/7/dataset_2077dcfe-ada7-4f6f-8f2d-afcb40eba271_files:/galaxy/server/database/objects/2/0/7/dataset_2077dcfe-ada7-4f6f-8f2d-afcb40eba271.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_gp3wtaog\"", + "files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"paired_end_merged_errors.fastqsanger\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ylsngg1i\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"fastqsanger\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "912c8bbec206c1f8", + "src": "hda", + "uuid": "2077dcfe-ada7-4f6f-8f2d-afcb40eba271" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/c676976b61076d41.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/c676976b61076d41.json new file mode 100644 index 000000000..58f4cd5b1 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/c676976b61076d41.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "c676976b61076d41", + "history_id": "3cbec5b19229f469", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T18:55:54.468666", + "update_time": "2024-09-04T18:56:51.677922", + "galaxy_version": "24.1", + "external_id": "gxy-pv96r", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/92/registry.xml' '/galaxy/server/database/jobs_directory/000/92/upload_params.json' '135:/galaxy/server/database/objects/0/5/f/dataset_05fef8c4-b17f-4f2e-8c5e-44f1ce3d2522_files:/galaxy/server/database/objects/0/5/f/dataset_05fef8c4-b17f-4f2e-8c5e-44f1ce3d2522.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_5snho320\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"Mut1.counts\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_9ld_su7j\", \"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": "c4029a77e6fda276", + "src": "hda", + "uuid": "05fef8c4-b17f-4f2e-8c5e-44f1ce3d2522" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/ca8200a9c07f5244.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/ca8200a9c07f5244.json new file mode 100644 index 000000000..4244500e5 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/ca8200a9c07f5244.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "ca8200a9c07f5244", + "history_id": "3cbec5b19229f469", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T19:22:50.733688", + "update_time": "2024-09-04T19:23:00.723357", + "galaxy_version": "24.1", + "external_id": "gxy-bz7hn", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/160/registry.xml' '/galaxy/server/database/jobs_directory/000/160/upload_params.json' '242:/galaxy/server/database/objects/2/3/7/dataset_237e6b05-bc7f-47cd-8d23-ddea1828edfa_files:/galaxy/server/database/objects/2/3/7/dataset_237e6b05-bc7f-47cd-8d23-ddea1828edfa.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_ap1rbzec\"", + "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"ensembl_ids.tab\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_gl6ae5u4\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"tabular\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "33276b55320b185c", + "src": "hda", + "uuid": "237e6b05-bc7f-47cd-8d23-ddea1828edfa" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/ce798158709471b6.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/ce798158709471b6.json new file mode 100644 index 000000000..42b316647 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/ce798158709471b6.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "ce798158709471b6", + "history_id": "3cbec5b19229f469", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T19:20:05.829785", + "update_time": "2024-09-04T19:20:17.218296", + "galaxy_version": "24.1", + "external_id": "gxy-fxjpg", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/153/registry.xml' '/galaxy/server/database/jobs_directory/000/153/upload_params.json' '234:/galaxy/server/database/objects/3/3/e/dataset_33ed6676-90ec-4afe-be79-634aff1c049a_files:/galaxy/server/database/objects/3/3/e/dataset_33ed6676-90ec-4afe-be79-634aff1c049a.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_m_bk_kdw\"", + "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"ensembl_ids.tab\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_0jjb603h\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"tabular\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "2f98a9c2980abc06", + "src": "hda", + "uuid": "33ed6676-90ec-4afe-be79-634aff1c049a" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/d3dd358c0a8193fa.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/d3dd358c0a8193fa.json new file mode 100644 index 000000000..5aabe6a1e --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/d3dd358c0a8193fa.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "d3dd358c0a8193fa", + "history_id": "3cbec5b19229f469", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T19:24:51.953357", + "update_time": "2024-09-04T19:25:02.445137", + "galaxy_version": "24.1", + "external_id": "gxy-w8gfq", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/169/registry.xml' '/galaxy/server/database/jobs_directory/000/169/upload_params.json' '251:/galaxy/server/database/objects/b/8/4/dataset_b84cd23b-f1b4-48a8-973c-6ae70ae1e45b_files:/galaxy/server/database/objects/b/8/4/dataset_b84cd23b-f1b4-48a8-973c-6ae70ae1e45b.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_db3t9n4h\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"file1.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_12anq3fx\", \"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": "19133157b7774ae6", + "src": "hda", + "uuid": "b84cd23b-f1b4-48a8-973c-6ae70ae1e45b" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/efdc907f4a8e4544.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/efdc907f4a8e4544.json new file mode 100644 index 000000000..cc7311321 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/efdc907f4a8e4544.json @@ -0,0 +1,67 @@ +{ + "model_class": "Job", + "id": "efdc907f4a8e4544", + "history_id": "3cbec5b19229f469", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T18:37:21.127148", + "update_time": "2024-09-04T18:37:47.806755", + "galaxy_version": "24.1", + "external_id": "gxy-j5jbq", + "handler": null, + "job_runner_name": null, + "command_line": "mummer -l '20' -b -threads ${GALAXY_SLOTS:-1} -qthreads ${GALAXY_SLOTS:-1} '/galaxy/server/database/objects/5/c/7/dataset_5c778596-6f7c-4484-a34c-c1d1f1d62b82.dat' '/galaxy/server/database/objects/7/6/b/dataset_76bbb1a6-c800-4cf0-8e9e-71c76ff5ed94.dat' > '/galaxy/server/database/objects/7/1/1/dataset_71196343-4536-4f57-ba54-12b66aeecaf3.dat' && mummerplot -b '20' -s 'small' -terminal png -title 'Title' '/galaxy/server/database/objects/7/1/1/dataset_71196343-4536-4f57-ba54-12b66aeecaf3.dat' && gnuplot < out.gp", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"fasta\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "mumplot": "{\"__current_case__\": 0, \"breaklen\": \"20\", \"color\": \"\", \"coverage\": \"\", \"fat\": false, \"filter\": false, \"labels\": {\"IDs\": \"no\", \"__current_case__\": 1}, \"plot\": \"yes\", \"range\": {\"__current_case__\": 1, \"custom\": \"no\"}, \"size\": \"small\", \"snp\": false, \"title\": \"Title\"}", + "options": "{\"__current_case__\": 1, \"advanced\": \"defaults\"}", + "position": "false", + "substring": "false", + "print_length": "false", + "chars": "false", + "force": "false", + "direction": "\"-b\"", + "min": "\"20\"", + "anchoring": "\"\"" + }, + "inputs": { + "reference_sequence": { + "id": "796d7152b6f678c7", + "src": "hda", + "uuid": "5c778596-6f7c-4484-a34c-c1d1f1d62b82" + }, + "query_sequence": { + "id": "3352612fbd760959", + "src": "hda", + "uuid": "76bbb1a6-c800-4cf0-8e9e-71c76ff5ed94" + } + }, + "outputs": { + "output": { + "id": "2cd83bd6d67a678e", + "src": "hda", + "uuid": "71196343-4536-4f57-ba54-12b66aeecaf3" + }, + "png_output": { + "id": "3a48336881d2edb3", + "src": "hda", + "uuid": "4c7ccdc2-b6ec-40b6-bb8b-09c9edd0ff8c" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "gnuplot 5.2 patchlevel 7\n", + "tool_stderr": "Reading mummer file /galaxy/server/database/objects/7/1/1/dataset_71196343-4536-4f57-ba54-12b66aeecaf3.dat (use mummer -c)\nWriting plot files out.fplot, out.rplot, out.hplot\nWriting gnuplot script out.gp\nRendering plot out.png\nWARNING: Unable to run 'false out.gp', Inappropriate ioctl for device\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "gnuplot 5.2 patchlevel 7\n", + "stderr": "Reading mummer file /galaxy/server/database/objects/7/1/1/dataset_71196343-4536-4f57-ba54-12b66aeecaf3.dat (use mummer -c)\nWriting plot files out.fplot, out.rplot, out.hplot\nWriting gnuplot script out.gp\nRendering plot out.png\nWARNING: Unable to run 'false out.gp', Inappropriate ioctl for device\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/f263adfadf1d211f.json b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/f263adfadf1d211f.json new file mode 100644 index 000000000..9c0beb69b --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/errors/f263adfadf1d211f.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "f263adfadf1d211f", + "history_id": "3cbec5b19229f469", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-04T19:25:03.581244", + "update_time": "2024-09-04T19:25:13.817519", + "galaxy_version": "24.1", + "external_id": "gxy-56pjj", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/171/registry.xml' '/galaxy/server/database/jobs_directory/000/171/upload_params.json' '253:/galaxy/server/database/objects/b/3/e/dataset_b3e73fc3-8614-4e87-9224-8396c0efb062_files:/galaxy/server/database/objects/b/3/e/dataset_b3e73fc3-8614-4e87-9224-8396c0efb062.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_jvsh0z7f\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"file1.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_j3zzejw6\", \"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": "f4867a6ed8754f77", + "src": "hda", + "uuid": "b3e73fc3-8614-4e87-9224-8396c0efb062" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/job-metrics.csv b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/job-metrics.csv new file mode 100644 index 000000000..752e11686 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/job-metrics.csv @@ -0,0 +1,206 @@ +id,history_id,history_name,state,tool_id,invocation_id,workflow_id,cpuacct.usage,galaxy_memory_mb,galaxy_slots,memory.limit_in_bytes,memory.peak,memory.soft_limit_in_bytes,memtotal,processor_count,runtime_seconds 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2024-09-04T19:24:39.539111 toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0 +996a241e7cda9c62 ok 2024-09-04T19:24:23.738016 upload1 +56f34d6fb72980c7 ok 2024-09-04T19:24:22.623739 upload1 +09976a7dbbbe05e4 error 2024-09-04T19:24:03.542977 upload1 +d5dacb7eaf50df39 ok 2024-09-04T19:23:50.253730 toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1 +2ad37a77b3e1842f ok 2024-09-04T19:23:19.886977 upload1 +ca8200a9c07f5244 error 2024-09-04T19:23:00.723357 upload1 +7f033b59caa88f29 ok 2024-09-04T19:22:48.139859 toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1 +a65dd01535592a4a ok 2024-09-04T19:22:17.842787 upload1 +db35a4950115a8ea ok 2024-09-04T19:21:58.329346 toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1 +f0e2df4e46a48f04 ok 2024-09-04T19:21:28.945984 upload1 +db09421f3f1b1abc ok 2024-09-04T19:21:07.078840 toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1 +af4b407ead28586b ok 2024-09-04T19:20:36.514817 upload1 +ce798158709471b6 error 2024-09-04T19:20:17.218296 upload1 +9f10efce064423f0 ok 2024-09-04T19:20:03.017108 toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1 +323aee714abfe228 ok 2024-09-04T19:19:33.752433 upload1 +97e99b2c25552794 ok 2024-09-04T19:19:13.496103 toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1 +883203584e06040a ok 2024-09-04T19:18:19.484963 upload1 +44febf85122db16d ok 2024-09-04T19:17:54.566414 toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0 +870bfced8ad4ac5d ok 2024-09-04T19:17:12.064031 upload1 +dce29b8e275e623e ok 2024-09-04T19:16:49.610109 toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0 +a12469b263b84542 ok 2024-09-04T19:16:34.357388 upload1 +2652ae4d24003cae ok 2024-09-04T19:16:13.467537 toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0 +6a41048ca8f99318 ok 2024-09-04T19:15:58.093491 upload1 +4ce9828a66d14df3 error 2024-09-04T19:15:38.881060 upload1 +6486d0127152cd1a ok 2024-09-04T19:15:25.765048 toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0 +f6cb1a21fba08826 ok 2024-09-04T19:15:09.559872 upload1 +f777042bd482ff7f ok 2024-09-04T19:14:47.459366 toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0 +3248383e751a373f ok 2024-09-04T19:14:31.262072 upload1 +0a3ea1b885987c08 error 2024-09-04T19:14:10.613857 toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0 +6da00d8fe807ee3f ok 2024-09-04T19:14:01.505027 upload1 +c4029a77e6fda276 ok 2024-09-04T19:13:40.348497 toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0 +d51caf14cb05b163 ok 2024-09-04T19:13:03.593413 upload1 +509d4c4dc6597934 ok 2024-09-04T19:12:41.721920 toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy2 +58131dc761ac44d3 ok 2024-09-04T19:11:00.449499 upload1 +68b9659aa9ffacfa ok 2024-09-04T19:10:39.478069 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2024-09-04T18:36:34.769176 upload1 +3bc05048bf9ac1a4 ok 2024-09-04T18:36:06.764899 toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7 +d7567a01e2b6992a ok 2024-09-04T18:35:27.032089 upload1 +11c24c9aadb92cb2 ok 2024-09-04T18:35:03.718780 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5 +912c8bbec206c1f8 ok 2024-09-04T18:34:50.366693 upload1 +0ecf5896e74d14f4 ok 2024-09-04T18:34:27.475969 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5 +bc463e12e52d0ca9 ok 2024-09-04T18:34:14.999586 upload1 +6cb2c6ca63395177 error 2024-09-04T18:33:56.634551 upload1 +4c57e16f0544033d ok 2024-09-04T18:33:41.693605 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5 +5dce4c6ae032b20f ok 2024-09-04T18:33:23.267736 upload1 +25718ce0aef57e36 error 2024-09-04T18:33:03.041702 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"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": "annotatemyids/3.5.0.1-1", "has_data": true, "data": {"tool_id": "annotatemyids", "tool_version": "3.5.0.1", "test_index": 1, "time_seconds": 50.57112193107605, "inputs": {"id_file": {"src": "hda", "id": "e46983a82f9c39d6"}, "organism": "Hs", "id_type": "ENSEMBL", "rscriptOpt": true}, "job": {"model_class": "Job", "id": "7f033b59caa88f29", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:22:18.390978", "update_time": "2024-09-04T19:22:48.139859", "galaxy_version": "24.1", "external_id": "gxy-v4jvx", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/jobs_directory/000/159/configs/tmp8rnur25c' '/galaxy/server/database/objects/7/c/0/dataset_7c04c587-142d-404c-a0bb-9cc760c6255b.dat' && Rscript '/galaxy/server/database/jobs_directory/000/159/configs/tmp8rnur25c'", "user_email": "tests@fake.org", "command_version": "R version 3.4.1 (2017-06-30) -- \"Single Candle\", org.Hs.eg.db version 3.5.0, org.Dr.eg.db version 3.5.0, org.Dm.eg.db version 3.5.0, org.Mm.eg.db version 3.5.0", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "rscriptOpt": "true", "remove_dups": "false", "output_cols": "[\"ENSEMBL\", \"ENTREZID\", \"SYMBOL\", \"GENENAME\"]", "id_type": "\"ENSEMBL\"", "organism": "\"Hs\"", "file_has_header": "false"}, "inputs": {"id_file": {"id": "e46983a82f9c39d6", "src": "hda", "uuid": "f66d89cd-d3c4-48cf-a1db-6a5d5bbb6b79"}}, "outputs": {"out_tab": {"id": "9ca98a658a77e406", "src": "hda", "uuid": "1c588856-5eaf-486c-b88a-f51821ccd043"}, "out_rscript": {"id": "8a7ca2773bfa8b1b", "src": "hda", "uuid": "7c04c587-142d-404c-a0bb-9cc760c6255b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:1 mapping between keys and columns\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:1 mapping between keys and columns\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "17 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "17.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:22:37", "plugin": "core", "name": "end_epoch", "raw_value": "1725477757.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:22:20", "plugin": "core", "name": "start_epoch", "raw_value": "1725477740.0000000"}, {"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": "annotatemyids/3.5.0.1-2", "has_data": true, "data": {"tool_id": "annotatemyids", "tool_version": "3.5.0.1", "test_index": 2, "time_seconds": 12.166870594024658, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "annotatemyids/3.5.0.1-2", "has_data": true, "data": {"tool_id": "annotatemyids", "tool_version": "3.5.0.1", "test_index": 2, "time_seconds": 10.907672882080078, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "annotatemyids/3.5.0.1-3", "has_data": true, "data": {"tool_id": "annotatemyids", "tool_version": "3.5.0.1", "test_index": 3, "time_seconds": 50.51839232444763, "inputs": {"id_file": {"src": "hda", "id": "666fb8d800955959"}, "organism": "Hs", "id_type": "ENSEMBL", "output_cols": ["ENSEMBL", "GO", "ONTOLOGY", "EVIDENCE"], "remove_dups": true}, "job": {"model_class": "Job", "id": "db09421f3f1b1abc", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:20:36.860793", "update_time": "2024-09-04T19:21:07.078840", "galaxy_version": "24.1", "external_id": "gxy-ptnwc", "handler": null, "job_runner_name": null, "command_line": "Rscript '/galaxy/server/database/jobs_directory/000/155/configs/tmp7fbhb2pi'", "user_email": "tests@fake.org", "command_version": "R version 3.4.1 (2017-06-30) -- \"Single Candle\", org.Hs.eg.db version 3.5.0, org.Dr.eg.db version 3.5.0, org.Dm.eg.db version 3.5.0, org.Mm.eg.db version 3.5.0", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "rscriptOpt": "false", "remove_dups": "true", "output_cols": "[\"ENSEMBL\", \"GO\", \"ONTOLOGY\", \"EVIDENCE\"]", "id_type": "\"ENSEMBL\"", "organism": "\"Hs\"", "file_has_header": "false"}, "inputs": {"id_file": {"id": "666fb8d800955959", "src": "hda", "uuid": "a4e12e73-1825-4b30-a6d1-07b8764a2425"}}, "outputs": {"out_tab": {"id": "bf20728f182d322f", "src": "hda", "uuid": "33389d11-7c83-46b9-9231-779d523cf250"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:many mapping between keys and columns\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:many mapping between keys and columns\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "18 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "18.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:20:56", "plugin": "core", "name": "end_epoch", "raw_value": "1725477656.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:20:38", "plugin": "core", "name": "start_epoch", "raw_value": "1725477638.0000000"}, {"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": "annotatemyids/3.5.0.1-3", "has_data": true, "data": {"tool_id": "annotatemyids", "tool_version": "3.5.0.1", "test_index": 3, "time_seconds": 50.144646883010864, "inputs": {"id_file": {"src": "hda", "id": "74521839f0a756d3"}, "organism": "Hs", "id_type": "ENSEMBL", "output_cols": ["ENSEMBL", "GO", "ONTOLOGY", "EVIDENCE"], "remove_dups": true}, "job": {"model_class": "Job", "id": "d5dacb7eaf50df39", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:23:20.141346", "update_time": "2024-09-04T19:23:50.253730", "galaxy_version": "24.1", "external_id": "gxy-lbnmm", "handler": null, "job_runner_name": null, "command_line": "Rscript '/galaxy/server/database/jobs_directory/000/162/configs/tmp71xpqud2'", "user_email": "tests@fake.org", "command_version": "R version 3.4.1 (2017-06-30) -- \"Single Candle\", org.Hs.eg.db version 3.5.0, org.Dr.eg.db version 3.5.0, org.Dm.eg.db version 3.5.0, org.Mm.eg.db version 3.5.0", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "rscriptOpt": "false", "remove_dups": "true", "output_cols": "[\"ENSEMBL\", \"GO\", \"ONTOLOGY\", \"EVIDENCE\"]", "id_type": "\"ENSEMBL\"", "organism": "\"Hs\"", "file_has_header": "false"}, "inputs": {"id_file": {"id": "74521839f0a756d3", "src": "hda", "uuid": "aa3977e9-2693-4a69-94bf-37e5ec8bc114"}}, "outputs": {"out_tab": {"id": "6262ea5a538b376b", "src": "hda", "uuid": "9d41c73b-71cb-4e3e-b606-6e0868fa59f0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:many mapping between keys and columns\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Warning message:\nIn Sys.setlocale(\"LC_MESSAGES\", \"en_US.UTF-8\") :\n OS reports request to set locale to \"en_US.UTF-8\" cannot be honored\n'select()' returned 1:many mapping between keys and columns\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "18 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "18.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:23:39", "plugin": "core", "name": "end_epoch", "raw_value": "1725477819.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:23:21", "plugin": "core", "name": "start_epoch", "raw_value": "1725477801.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_consensus/1.10+galaxy1-0", "has_data": true, "data": {"tool_id": "bcftools_consensus", "tool_version": "1.10+galaxy1", "test_index": 0, "time_seconds": 44.202178955078125, "inputs": {"input_file": {"src": "hda", "id": "30414a2a4d294422"}, "reference_source|fasta_ref": {"src": "hda", "id": "1ca2e2286b408b79"}, "reference_source|reference_source_selector": "history", "sec_default|mask": {"src": "hda", "id": "60d24ccfdaf155a1"}, "chain": true}, "job": {"model_class": "Job", "id": "d4dd1537b5f85bb9", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:26:11.833942", "update_time": "2024-09-04T19:26:30.098924", "galaxy_version": "24.1", "external_id": "gxy-s5mx8", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/4/b/7/dataset_4b761d13-ca69-4761-bb22-22c94ed59c29.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/3/4/a/dataset_34a62a11-fe42-48c1-ab7b-4c829be5436e.dat' ref.fa && samtools faidx ref.fa && bcftools consensus --fasta-ref ref.fa --mask '/galaxy/server/database/objects/9/d/e/dataset_9ded083b-713a-46d3-96a6-bc6824a7554a.dat' --chain '/galaxy/server/database/objects/9/b/5/dataset_9b5949b1-347d-4b92-baee-39744405a113.dat' --output '/galaxy/server/database/objects/7/9/3/dataset_7937c90d-6bf9-4bc3-889c-ccbff3ca7a52.dat' input.vcf.gz", "user_email": "tests@fake.org", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_restrict": "{\"exclude\": null, \"include\": null}", "rename": "false", "chain": "true", "sec_default": "{\"iupac_codes\": false, \"mask\": {\"values\": [{\"id\": 260, \"src\": \"hda\"}]}, \"sample\": null, \"select_haplotype\": null}", "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 259, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_file": {"id": "30414a2a4d294422", "src": "hda", "uuid": "4b761d13-ca69-4761-bb22-22c94ed59c29"}, "reference_source|fasta_ref": {"id": "1ca2e2286b408b79", "src": "hda", "uuid": "34a62a11-fe42-48c1-ab7b-4c829be5436e"}, "sec_default|mask": {"id": "60d24ccfdaf155a1", "src": "hda", "uuid": "9ded083b-713a-46d3-96a6-bc6824a7554a"}}, "outputs": {"output_file": {"id": "2aa75a08ff7157b6", "src": "hda", "uuid": "7937c90d-6bf9-4bc3-889c-ccbff3ca7a52"}, "chain_file": {"id": "609c5fe74193a1bd", "src": "hda", "uuid": "9b5949b1-347d-4b92-baee-39744405a113"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 12 variants\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 12 variants\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-04 19:26:17", "plugin": "core", "name": "end_epoch", "raw_value": "1725477977.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:26:17", "plugin": "core", "name": "start_epoch", "raw_value": "1725477977.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_consensus/1.10+galaxy1-1", "has_data": true, "data": {"tool_id": "bcftools_consensus", "tool_version": "1.10+galaxy1", "test_index": 1, "status": "skip"}}, {"id": "bcftools_consensus/1.10+galaxy1-2", "has_data": true, "data": {"tool_id": "bcftools_consensus", "tool_version": "1.10+galaxy1", "test_index": 2, "time_seconds": 37.60496401786804, "inputs": {"input_file": {"src": "hda", "id": "2b8f4be41e46fdea"}, "reference_source|fasta_ref": {"src": "hda", "id": "b8e41ea11f11d56e"}, "reference_source|reference_source_selector": "history", "sec_default|mask": {"src": "hda", "id": "0369a2e1aa546eeb"}, "chain": false, "rename": true}, "job": {"model_class": "Job", "id": "e03d301d94ebae59", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:26:55.352477", "update_time": "2024-09-04T19:27:08.838184", "galaxy_version": "24.1", "external_id": "gxy-hlncm", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/a/1/e/dataset_a1e44f52-2f9d-425f-8ade-95c667922a13.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/f/3/8/dataset_f388440e-9a00-438a-8dd5-0ff7aaa5c933.dat' ref.fa && samtools faidx ref.fa && bcftools consensus --fasta-ref ref.fa --mask '/galaxy/server/database/objects/1/7/8/dataset_17818e7c-6e29-48a2-91d0-0c8b6a0c8223.dat' input.vcf.gz | awk 'BEGIN {i=1} {if (match($0, /^>/)) {if (i==1) {name=\"consensus.vcf\"} else {name=sprintf(\"%s-%d\",\"consensus.vcf\",i);} print(gensub(/>[^ ]+( ?.*)/, \">\" name \"\\\\1\", 1)); i=i+1;} else {print}}' > '/galaxy/server/database/objects/6/4/a/dataset_64a436b9-f4b5-47b4-8519-a900af553007.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_restrict": "{\"exclude\": null, \"include\": null}", "rename": "true", "chain": "false", "sec_default": "{\"iupac_codes\": false, \"mask\": {\"values\": [{\"id\": 265, \"src\": \"hda\"}]}, \"sample\": null, \"select_haplotype\": null}", "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 264, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_file": {"id": "2b8f4be41e46fdea", "src": "hda", "uuid": "a1e44f52-2f9d-425f-8ade-95c667922a13"}, "reference_source|fasta_ref": {"id": "b8e41ea11f11d56e", "src": "hda", "uuid": "f388440e-9a00-438a-8dd5-0ff7aaa5c933"}, "sec_default|mask": {"id": "0369a2e1aa546eeb", "src": "hda", "uuid": "17818e7c-6e29-48a2-91d0-0c8b6a0c8223"}}, "outputs": {"output_file": {"id": "c22a2fc56c552f5f", "src": "hda", "uuid": "64a436b9-f4b5-47b4-8519-a900af553007"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 12 variants\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 12 variants\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-04 19:26:57", "plugin": "core", "name": "end_epoch", "raw_value": "1725478017.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:26:57", "plugin": "core", "name": "start_epoch", "raw_value": "1725478017.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_consensus/1.10+galaxy1-3", "has_data": true, "data": {"tool_id": "bcftools_consensus", "tool_version": "1.10+galaxy1", "test_index": 3, "time_seconds": 33.53839087486267, "inputs": {"input_file": {"src": "hda", "id": "db343bee3fe9f12c"}, "reference_source|fasta_ref": {"src": "hda", "id": "1db56fca77ae2623"}, "reference_source|reference_source_selector": "history", "sec_restrict|include": "TYPE=\"snp\""}, "job": {"model_class": "Job", "id": "29b611a81539b714", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:27:29.521001", "update_time": "2024-09-04T19:27:42.251927", "galaxy_version": "24.1", "external_id": "gxy-2vwf6", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/c/c/dataset_8cc91dcf-678b-4c23-9055-9d2ad8e7d50e.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/a/2/8/dataset_a28fff7f-b0b7-4293-8a08-1bb23253c248.dat' ref.fa && samtools faidx ref.fa && bcftools consensus --fasta-ref ref.fa --include 'TYPE=\"snp\"' --output '/galaxy/server/database/objects/d/8/3/dataset_d8352ac8-ad1e-4c4f-92ee-c3729e99ba7c.dat' input.vcf.gz", "user_email": "tests@fake.org", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_restrict": "{\"exclude\": null, \"include\": \"TYPE=\\\"snp\\\"\"}", "rename": "false", "chain": "false", "sec_default": "{\"iupac_codes\": false, \"mask\": null, \"sample\": null, \"select_haplotype\": null}", "reference_source": "{\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 268, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"input_file": {"id": "db343bee3fe9f12c", "src": "hda", "uuid": "8cc91dcf-678b-4c23-9055-9d2ad8e7d50e"}, "reference_source|fasta_ref": {"id": "1db56fca77ae2623", "src": "hda", "uuid": "a28fff7f-b0b7-4293-8a08-1bb23253c248"}}, "outputs": {"output_file": {"id": "8ee52624f2b28ffe", "src": "hda", "uuid": "d8352ac8-ad1e-4c4f-92ee-c3729e99ba7c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 6 variants\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Note: the --sample option not given, applying all records regardless of the genotype\nThe site 1:5 overlaps with another variant, skipping...\nApplied 6 variants\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-04 19:27:31", "plugin": "core", "name": "end_epoch", "raw_value": "1725478051.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:27:31", "plugin": "core", "name": "start_epoch", "raw_value": "1725478051.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_plugin_impute_info/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_plugin_impute_info", "tool_version": "1.10", "test_index": 0, "time_seconds": 39.133519411087036, "inputs": {"input_file": {"src": "hda", "id": "28b32e085ccb1b89"}, "output_type": "v"}, "job": {"model_class": "Job", "id": "3fff9e3a34464297", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_impute_info/bcftools_plugin_impute_info/1.10", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:28:03.197883", "update_time": "2024-09-04T19:28:22.816929", "galaxy_version": "24.1", "external_id": "gxy-dgwjq", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/9/e/d/dataset_9ede5ac6-3638-4395-b035-25c5d9dd72b0.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin impute-info --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/1/8/3/dataset_18301daf-9437-4c55-9186-be6dc0a8c630.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_restrict": "{\"exclude\": null, \"include\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}"}, "inputs": {"input_file": {"id": "28b32e085ccb1b89", "src": "hda", "uuid": "9ede5ac6-3638-4395-b035-25c5d9dd72b0"}}, "outputs": {"output_file": {"id": "04ab4ec023cb8a0f", "src": "hda", "uuid": "18301daf-9437-4c55-9186-be6dc0a8c630"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[impute-info.c] Warning: info tag not added to sites that are not biallelic diploid\nLines total/info-added/unchanged-no-tag/unchanged-not-biallelic-diploid:\t33/32/0/1\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[impute-info.c] Warning: info tag not added to sites that are not biallelic diploid\nLines total/info-added/unchanged-no-tag/unchanged-not-biallelic-diploid:\t33/32/0/1\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:28:10", "plugin": "core", "name": "end_epoch", "raw_value": "1725478090.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:28:09", "plugin": "core", "name": "start_epoch", "raw_value": "1725478089.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_query/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_query", "tool_version": "1.10", "test_index": 0, "time_seconds": 32.3508198261261, "inputs": {"input_files": {"src": "hda", "id": "9f960015bf293d85"}, "sec_query|format": "%CHROM\\t%POS\\t%REF\\t%ALT\\t%DP4\\t%AN[\\t%GT\\t%TGT]\\n", "sec_query|tsv": true}, "job": {"model_class": "Job", "id": "ea5905d72308f49c", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.10", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:28:43.738004", "update_time": "2024-09-04T19:28:56.130080", "galaxy_version": "24.1", "external_id": "gxy-j8mvg", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/8/5/5/dataset_85508f9e-1cfa-4f7c-a3d6-f3e96c2c6640.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bcftools query --format '%CHROM\\t%POS\\t%REF\\t%ALT\\t%DP4\\t%AN[\\t%GT\\t%TGT]\\n' --vcf-list vcfs_list > /galaxy/server/database/objects/e/2/8/dataset_e2858eb4-5a65-4408-8d2d-4834aa6682c2.dat", "user_email": "tests@fake.org", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "sec_query": "{\"allow_undef_tags\": false, \"format\": \"%CHROM\\\\t%POS\\\\t%REF\\\\t%ALT\\\\t%DP4\\\\t%AN[\\\\t%GT\\\\t%TGT]\\\\n\", \"print_header\": false, \"tsv\": true}", "sec_restrict": "{\"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}"}, "inputs": {"input_files": {"id": "9f960015bf293d85", "src": "hda", "uuid": "85508f9e-1cfa-4f7c-a3d6-f3e96c2c6640"}, "input_files1": {"id": "9f960015bf293d85", "src": "hda", "uuid": "85508f9e-1cfa-4f7c-a3d6-f3e96c2c6640"}}, "outputs": {"output_file": {"id": "10e4387d1c5decf3", "src": "hda", "uuid": "e2858eb4-5a65-4408-8d2d-4834aa6682c2"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:28:46", "plugin": "core", "name": "end_epoch", "raw_value": "1725478126.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:28:45", "plugin": "core", "name": "start_epoch", "raw_value": "1725478125.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "circos/0.69.8+galaxy7-0", "has_data": true, "data": {"tool_id": "circos", "tool_version": "0.69.8+galaxy7", "test_index": 0, "time_seconds": 59.80747032165527, "inputs": {"reference_genome|ref|genome_fasta": {"src": "hda", "id": "efdc907f4a8e4544"}, "reference_genome|ref|ref_source": "history", "outputs|png": true, "outputs|svg": true}, "job": {"model_class": "Job", "id": "3bc05048bf9ac1a4", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T18:35:27.424165", "update_time": "2024-09-04T18:36:06.764899", "galaxy_version": "24.1", "external_id": "gxy-792zf", "handler": null, "job_runner_name": null, "command_line": "mkdir -p circos/conf/ circos/data/ && ln -s '/galaxy/server/database/objects/7/0/5/dataset_70561682-92fb-4277-8685-1cfdb88b50af.dat' genomeref.fa && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/circos/df7356989ac1/circos/karyotype-from-fasta.py' genomeref.fa > circos/conf/karyotype.txt && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/circos/df7356989ac1/circos/karyotype-colors.py' `grep -c '^chr\\s' 'circos/conf/karyotype.txt'` > 'circos/conf/karyotype-colors.conf' && touch circos/conf/karyotype-colors.conf && cp '/galaxy/server/database/jobs_directory/000/14/configs/tmpq0o052vg' circos/conf/circos.conf && cp '/galaxy/server/database/jobs_directory/000/14/configs/tmpm99x5c1j' circos/conf/ticks.conf && cp '/galaxy/server/database/jobs_directory/000/14/configs/tmpdlp22cyq' circos/conf/ideogram.conf && cp '/galaxy/server/database/jobs_directory/000/14/configs/tmpj_j0ivs9' circos/conf/data.conf && cp '/galaxy/server/database/jobs_directory/000/14/configs/tmpb4_iwt8u' circos/conf/links.conf && cp '/galaxy/server/database/jobs_directory/000/14/configs/tmp7acwdbp5' circos/conf/galaxy_test_case.json && circos -conf circos/conf/circos.conf -noparanoid", "user_email": "tests@fake.org", "command_version": "circos | v 0.69-8 | 15 Jun 2019 | Perl 5.026002", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "outputs": "{\"png\": true, \"svg\": true, \"tar\": false}", "limits": "{\"max_ideograms\": \"200\", \"max_links\": \"25000\", \"max_points_per_track\": \"25000\", \"max_ticks\": \"5000\"}", "ticks": "{\"radius\": \"1.0\", \"skip_first_label\": false, \"skip_last_label\": false, \"tick_group\": []}", "scaling": "{\"zooms\": []}", "sec_links": "{\"data\": []}", "sec_tdd": "{\"data\": []}", "plot_options": "{\"background\": {\"__current_case__\": 1, \"background_color\": \"#ffffff\", \"background_select\": \"color\"}, \"colour_profile\": null, \"radius\": \"1500\"}", "ideogram": "{\"angle_offset\": \"-90\", \"angle_orientation\": \"clockwise\", \"bands\": {\"band_stroke_color\": \"#000000\", \"band_stroke_thickness\": \"0\", \"band_transparency\": \"3\", \"fill_bands\": true, \"show_bands\": true}, \"chromosomes_reverse\": null, \"ideogram_labels\": {\"parallel\": true, \"radius_offset\": \"0.075\", \"show_label\": true, \"size\": \"24\"}, \"limit_chromosomes\": null, \"pairwise_spacing\": [], \"radius\": \"0.9\", \"spacing\": \"0.5\", \"thickness\": \"30.0\", \"units\": \"mb\"}", "reference_genome": "{\"ref\": {\"__current_case__\": 2, \"genome_fasta\": {\"values\": [{\"id\": 22, \"src\": \"hda\"}]}, \"ref_source\": \"history\"}}"}, "inputs": {"reference_genome|ref|genome_fasta": {"id": "efdc907f4a8e4544", "src": "hda", "uuid": "70561682-92fb-4277-8685-1cfdb88b50af"}}, "outputs": {"output_png": {"id": "195726d977b39d17", "src": "hda", "uuid": "4a90ccc0-43ba-49fc-b786-b2a5465227fa"}, "output_svg": {"id": "630aba36b9eb5918", "src": "hda", "uuid": "46d265a7-7203-45d6-a979-cd912d8ed99d"}, "karyotype_txt": {"id": "e98bd7369e82dc53", "src": "hda", "uuid": "fb4cfc46-faff-42f8-a511-7ff09956feb2"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "debuggroup summary 0.13s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002\ndebuggroup summary 0.13s current working directory /galaxy/server/database/jobs_directory/000/14/working\ndebuggroup summary 0.13s command /usr/local/bin/circos -conf circos/conf/circos.conf -noparanoid\ndebuggroup summary 0.13s loading configuration from file circos/conf/circos.conf\ndebuggroup summary 0.13s found conf file circos/conf/circos.conf\ndebuggroup summary 0.23s debug will appear for these features: output,summary\ndebuggroup summary 0.23s bitmap output image ./circos.png\ndebuggroup summary 0.23s SVG output image ./circos.svg\ndebuggroup summary 0.23s parsing karyotype and organizing ideograms\ndebuggroup summary 0.24s karyotype has 2 chromosomes of total size 56,082\ndebuggroup summary 0.24s applying global and local scaling\ndebuggroup summary 0.24s allocating image, colors and brushes\ndebuggroup summary 4.95s drawing 2 ideograms of total size 56,082\ndebuggroup summary 4.95s drawing highlights and ideograms\ndebuggroup output 4.95s generating output\ndebuggroup output 5.24s created PNG image ./circos.png (40 kb)\ndebuggroup output 5.25s created SVG image ./circos.svg (2 kb)\n", "tool_stderr": "Use of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\n", "job_stdout": "", "job_stderr": "", "stdout": "debuggroup summary 0.13s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002\ndebuggroup summary 0.13s current working directory /galaxy/server/database/jobs_directory/000/14/working\ndebuggroup summary 0.13s command /usr/local/bin/circos -conf circos/conf/circos.conf -noparanoid\ndebuggroup summary 0.13s loading configuration from file circos/conf/circos.conf\ndebuggroup summary 0.13s found conf file circos/conf/circos.conf\ndebuggroup summary 0.23s debug will appear for these features: output,summary\ndebuggroup summary 0.23s bitmap output image ./circos.png\ndebuggroup summary 0.23s SVG output image ./circos.svg\ndebuggroup summary 0.23s parsing karyotype and organizing ideograms\ndebuggroup summary 0.24s karyotype has 2 chromosomes of total size 56,082\ndebuggroup summary 0.24s applying global and local scaling\ndebuggroup summary 0.24s allocating image, colors and brushes\ndebuggroup summary 4.95s drawing 2 ideograms of total size 56,082\ndebuggroup summary 4.95s drawing highlights and ideograms\ndebuggroup output 4.95s generating output\ndebuggroup output 5.24s created PNG image ./circos.png (40 kb)\ndebuggroup output 5.25s created SVG image ./circos.svg (2 kb)\n", "stderr": "Use of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "10737", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "10737.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 18:35:44", "plugin": "core", "name": "start_epoch", "raw_value": "1725474944.0000000"}, {"title": "Job End Time", "value": "2024-09-04 18:35:50", "plugin": "core", "name": "end_epoch", "raw_value": "1725474950.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}]}, "status": "success"}}, {"id": "circos/0.69.8+galaxy7-1", "has_data": true, "data": {"tool_id": "circos", "tool_version": "0.69.8+galaxy7", "test_index": 1, "time_seconds": 49.82677865028381, "inputs": {"reference_genome|ref|genome_fasta": {"src": "hda", "id": "30329d3a85219f0d"}, "reference_genome|ref|ref_source": "history", "ideogram|units": "kb", "sec_tdd|data_0|r1": "0.9", "sec_tdd|data_0|r0": "0.8", "sec_tdd|data_0|plot_format|data_source": {"src": "hda", "id": "4a78e184316c9849"}, "sec_tdd|data_0|plot_format|plot_format_select": "histogram", "sec_tdd|data_1|r1": "0.8", "sec_tdd|data_1|r0": "0.7", "sec_tdd|data_1|plot_format|data_source": {"src": "hda", "id": "4a78e184316c9849"}, "sec_tdd|data_1|plot_format|plot_format_select": "scatter", "sec_tdd|data_2|r1": "0.7", "sec_tdd|data_2|r0": "0.6", "sec_tdd|data_2|plot_format|data_source": {"src": "hda", "id": "36fea06678d221ff"}, "sec_tdd|data_2|plot_format|plot_format_select": "tile", "sec_links|data_0|radius": "0.59", "sec_links|data_0|data_source": {"src": "hda", "id": "deea372bfaf13dbf"}, "sec_links|data_0|linktype|ribbon": "yes", "ticks|tick_group_0|spacing": "1", "ticks|tick_group_1|spacing": "5", "ticks|tick_group_1|ticks|format": "%.1f", "ticks|tick_group_1|ticks|show_tick_labels": "yes", "outputs|svg": true}, "job": {"model_class": "Job", "id": "6906245fd4fc934f", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T18:36:36.544934", "update_time": "2024-09-04T18:36:55.802438", "galaxy_version": "24.1", "external_id": "gxy-hjpf7", "handler": null, "job_runner_name": null, "command_line": "mkdir -p circos/conf/ circos/data/ && ln -s '/galaxy/server/database/objects/8/a/7/dataset_8a70ce72-be6b-4c16-bb70-4b18df1a8ab0.dat' genomeref.fa && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/circos/df7356989ac1/circos/karyotype-from-fasta.py' genomeref.fa > circos/conf/karyotype.txt && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/circos/df7356989ac1/circos/karyotype-colors.py' `grep -c '^chr\\s' 'circos/conf/karyotype.txt'` > 'circos/conf/karyotype-colors.conf' && touch circos/conf/karyotype-colors.conf && cp '/galaxy/server/database/jobs_directory/000/19/configs/tmp5tg1ftzd' circos/conf/circos.conf && cp '/galaxy/server/database/jobs_directory/000/19/configs/tmpxdcvxzsb' circos/conf/ticks.conf && cp '/galaxy/server/database/jobs_directory/000/19/configs/tmp6u7xadj0' circos/conf/ideogram.conf && cp '/galaxy/server/database/jobs_directory/000/19/configs/tmpkd7frchw' circos/conf/data.conf && cp '/galaxy/server/database/jobs_directory/000/19/configs/tmp5ug1dr45' circos/conf/links.conf && cp '/galaxy/server/database/jobs_directory/000/19/configs/tmpniw8d88_' circos/conf/galaxy_test_case.json && cp '/galaxy/server/database/objects/8/3/f/dataset_83f616cc-f234-45bc-9f8e-ce73211f06c6.dat' circos/data/data-0.txt && cp '/galaxy/server/database/objects/8/3/f/dataset_83f616cc-f234-45bc-9f8e-ce73211f06c6.dat' circos/data/data-1.txt && cp '/galaxy/server/database/objects/2/f/0/dataset_2f008baa-67f7-4d3a-9d90-28652f35d639.dat' circos/data/data-2.txt && cp '/galaxy/server/database/objects/9/5/a/dataset_95adab26-627e-42dd-910f-e605a98252f7.dat' circos/data/links-0.txt && circos -conf circos/conf/circos.conf -noparanoid", "user_email": "tests@fake.org", "command_version": "circos | v 0.69-8 | 15 Jun 2019 | Perl 5.026002", "params": {"reference_genome": "{\"ref\": {\"__current_case__\": 2, \"genome_fasta\": {\"values\": [{\"id\": 26, \"src\": \"hda\"}]}, \"ref_source\": \"history\"}}", "ideogram": "{\"angle_offset\": \"-90\", \"angle_orientation\": \"clockwise\", \"bands\": {\"band_stroke_color\": \"#000000\", \"band_stroke_thickness\": \"0\", \"band_transparency\": \"3\", \"fill_bands\": true, \"show_bands\": true}, \"chromosomes_reverse\": null, \"ideogram_labels\": {\"parallel\": true, \"radius_offset\": \"0.075\", \"show_label\": true, \"size\": \"24\"}, \"limit_chromosomes\": null, \"pairwise_spacing\": [], \"radius\": \"0.9\", \"spacing\": \"0.5\", \"thickness\": \"30.0\", \"units\": \"kb\"}", "plot_options": "{\"background\": {\"__current_case__\": 1, \"background_color\": \"#ffffff\", \"background_select\": \"color\"}, \"colour_profile\": null, \"radius\": \"1500\"}", "sec_tdd": "{\"data\": [{\"__index__\": 0, \"minmax\": {\"__current_case__\": 1, \"minmax_select\": \"no\"}, \"minsize\": \"0.0\", \"orientation\": false, \"plot_format\": {\"__current_case__\": 0, \"data_source\": {\"values\": [{\"id\": 27, \"src\": \"hda\"}]}, \"format_specific\": {\"extend_bins\": false, \"fill_color\": \"#ffdcfc\", \"fill_color_alpha\": \"1.0\", \"fill_under\": true, \"stroke_color\": \"#000000\", \"stroke_color_alpha\": \"1.0\", \"stroke_thickness\": \"1\"}, \"plot_format_select\": \"histogram\"}, \"r0\": \"0.8\", \"r1\": \"0.9\", \"sec_axes\": {\"axes\": [], \"only_if_data\": \"always\"}, \"sec_bkgs\": {\"backgrounds\": [], \"only_if_data\": \"always\"}, \"sec_rule\": {\"rules\": []}, \"zdepth\": \"0\"}, {\"__index__\": 1, \"minmax\": {\"__current_case__\": 1, \"minmax_select\": \"no\"}, \"minsize\": \"0.0\", \"orientation\": false, \"plot_format\": {\"__current_case__\": 5, \"data_source\": {\"values\": [{\"id\": 27, \"src\": \"hda\"}]}, \"format_specific\": {\"fill_color\": \"#555555\", \"fill_color_alpha\": \"1.0\", \"glyph\": \"circle\", \"glyph_size\": \"8\", \"stroke_color\": \"#000000\", \"stroke_color_alpha\": \"1.0\", \"stroke_thickness\": \"1\"}, \"plot_format_select\": \"scatter\"}, \"r0\": \"0.7\", \"r1\": \"0.8\", \"sec_axes\": {\"axes\": [], \"only_if_data\": \"always\"}, \"sec_bkgs\": {\"backgrounds\": [], \"only_if_data\": \"always\"}, \"sec_rule\": {\"rules\": []}, \"zdepth\": \"0\"}, {\"__index__\": 2, \"minmax\": {\"__current_case__\": 1, \"minmax_select\": \"no\"}, \"minsize\": \"0.0\", \"orientation\": false, \"plot_format\": {\"__current_case__\": 6, \"data_source\": {\"values\": [{\"id\": 28, \"src\": \"hda\"}]}, \"format_specific\": {\"fill_color\": \"#000000\", \"fill_color_alpha\": \"1.0\", \"layers\": \"15\", \"margin\": \"0.002\", \"overflow\": {\"__current_case__\": 0, \"overflow_behavior\": \"hide\"}, \"padding\": \"8.0\", \"stroke_color\": \"#000000\", \"stroke_color_alpha\": \"1.0\", \"stroke_thickness\": \"1\", \"thickness\": \"15.0\"}, \"plot_format_select\": \"tile\"}, \"r0\": \"0.6\", \"r1\": \"0.7\", \"sec_axes\": {\"axes\": [], \"only_if_data\": \"always\"}, \"sec_bkgs\": {\"backgrounds\": [], \"only_if_data\": \"always\"}, \"sec_rule\": {\"rules\": []}, \"zdepth\": \"0\"}]}", "sec_links": "{\"data\": [{\"__index__\": 0, \"advanced\": {\"bezier_radius_purity\": \"0.75\", \"crest\": \"0.5\", \"perturbation\": {\"__current_case__\": 1, \"perturb\": \"no\"}}, \"bezier_radius\": \"0.1\", \"color\": \"#000000\", \"color_alpha\": \"1.0\", \"data_source\": {\"values\": [{\"id\": 29, \"src\": \"hda\"}]}, \"linktype\": {\"__current_case__\": 0, \"pattern\": \"solid\", \"ribbon\": \"yes\", \"twist\": \"\"}, \"minsize\": \"0.0\", \"radius\": \"0.59\", \"sec_link_rule\": {\"rules\": []}, \"thickness\": \"15.0\", \"zdepth\": \"0\"}]}", "scaling": "{\"zooms\": []}", "ticks": "{\"radius\": \"1.0\", \"skip_first_label\": false, \"skip_last_label\": false, \"tick_group\": [{\"__index__\": 0, \"color\": \"#000000\", \"size\": \"10.0\", \"spacing\": \"1.0\", \"ticks\": {\"__current_case__\": 1, \"show_tick_labels\": \"no\"}}, {\"__index__\": 1, \"color\": \"#000000\", \"size\": \"10.0\", \"spacing\": \"5.0\", \"ticks\": {\"__current_case__\": 0, \"format\": \"%.1f\", \"format_ext\": true, \"label_offset\": \"10.0\", \"label_size\": \"20.0\", \"show_tick_labels\": \"yes\"}}]}", "limits": "{\"max_ideograms\": \"200\", \"max_links\": \"25000\", \"max_points_per_track\": \"25000\", \"max_ticks\": \"5000\"}", "outputs": "{\"png\": true, \"svg\": true, \"tar\": false}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fasta\""}, "inputs": {"sec_tdd|data_0|plot_format|data_source": {"id": "4a78e184316c9849", "src": "hda", "uuid": "83f616cc-f234-45bc-9f8e-ce73211f06c6"}, "sec_tdd|data_1|plot_format|data_source": {"id": "4a78e184316c9849", "src": "hda", "uuid": "83f616cc-f234-45bc-9f8e-ce73211f06c6"}, "reference_genome|ref|genome_fasta": {"id": "30329d3a85219f0d", "src": "hda", "uuid": "8a70ce72-be6b-4c16-bb70-4b18df1a8ab0"}, "sec_tdd|data_2|plot_format|data_source": {"id": "36fea06678d221ff", "src": "hda", "uuid": "2f008baa-67f7-4d3a-9d90-28652f35d639"}, "sec_links|data_0|data_source": {"id": "deea372bfaf13dbf", "src": "hda", "uuid": "95adab26-627e-42dd-910f-e605a98252f7"}}, "outputs": {"output_png": {"id": "abadc5621f631059", "src": "hda", "uuid": "8cfce789-c3b9-43d9-8b51-372c4857f41c"}, "output_svg": {"id": "d4e738aa6461d3d1", "src": "hda", "uuid": "e760543b-e0ba-4ef9-85f3-718d828520f9"}, "karyotype_txt": {"id": "fd91d043720b0fcf", "src": "hda", "uuid": "7a852daf-17c3-4c95-92c6-ef38373f1c28"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "debuggroup summary 0.12s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002\ndebuggroup summary 0.13s current working directory /galaxy/server/database/jobs_directory/000/19/working\ndebuggroup summary 0.13s command /usr/local/bin/circos -conf circos/conf/circos.conf -noparanoid\ndebuggroup summary 0.13s loading configuration from file circos/conf/circos.conf\ndebuggroup summary 0.13s found conf file circos/conf/circos.conf\ndebuggroup summary 0.23s debug will appear for these features: output,summary\ndebuggroup summary 0.23s bitmap output image ./circos.png\ndebuggroup summary 0.23s SVG output image ./circos.svg\ndebuggroup summary 0.23s parsing karyotype and organizing ideograms\ndebuggroup summary 0.24s karyotype has 2 chromosomes of total size 56,082\ndebuggroup summary 0.24s applying global and local scaling\ndebuggroup summary 0.24s allocating image, colors and brushes\ndebuggroup summary 4.78s drawing 2 ideograms of total size 56,082\ndebuggroup summary 4.78s drawing highlights and ideograms\ndebuggroup summary 4.82s found conf file /usr/local/bin/../etc/tracks/link.conf\ndebuggroup summary 4.82s process track_0 link circos/conf/../data/links-0.txt\ndebuggroup summary 4.83s drawing link track_0 z 0\ndebuggroup !circoswarning 4.86s Data point of type [link] [50000-50500] extended past end of ideogram [ctgA 0-50001]. This data point will be [trimmed].\ndebuggroup !circoswarning 4.86s Data point of type [link] [51000-51500] extended past end of ideogram [ctgA 0-50001]. This data point will be [hidden].\ndebuggroup summary 4.86s found conf file /usr/local/bin/../etc/tracks/histogram.conf\ndebuggroup summary 4.86s found conf file /usr/local/bin/../etc/tracks/scatter.conf\ndebuggroup summary 4.86s found conf file /usr/local/bin/../etc/tracks/tile.conf\ndebuggroup summary 4.86s processing track_0 histogram circos/conf/../data/data-0.txt\ndebuggroup summary 4.92s processing track_1 scatter circos/conf/../data/data-1.txt\ndebuggroup summary 5.04s processing track_2 tile circos/conf/../data/data-2.txt\ndebuggroup summary 5.05s drawing track_0 histogram z 0 data-0.txt orient out\ndebuggroup summary 5.06s found conf file /usr/local/bin/../etc/tracks/axis.conf\ndebuggroup summary 5.61s drawing track_1 scatter z 0 data-1.txt orient out\ndebuggroup summary 5.63s found conf file /usr/local/bin/../etc/tracks/axis.conf\ndebuggroup summary 5.78s drawing track_2 tile z 0 data-2.txt orient out\ndebuggroup summary 5.79s found conf file /usr/local/bin/../etc/tracks/axis.conf\ndebuggroup !circoswarning 5.92s Data point of type [tile] [3013-6130] extended past end of ideogram [ctgB 0-6079]. This data point will be [trimmed].\ndebuggroup output 5.93s generating output\ndebuggroup output 6.29s created PNG image ./circos.png (539 kb)\ndebuggroup output 6.30s created SVG image ./circos.svg (414 kb)\n", "tool_stderr": "Use of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\nUse of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\nUse of uninitialized value within %Circos::Error::GROUPERROR in uc at /usr/local/bin/../lib/Circos/Error.pm line 354, line 21.\nUse of uninitialized value within %Circos::Error::GROUPERROR in uc at /usr/local/bin/../lib/Circos/Error.pm line 354, line 21.\nUse of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781, line 21.\nUse of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\nUse of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\nUse of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781, line 1214.\nUse of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\nUse of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\nUse of uninitialized value within %Circos::Error::GROUPERROR in uc at /usr/local/bin/../lib/Circos/Error.pm line 354.\n", "job_stdout": "", "job_stderr": "", "stdout": "debuggroup summary 0.12s welcome to circos v0.69-8 15 Jun 2019 on Perl 5.026002\ndebuggroup summary 0.13s current working directory /galaxy/server/database/jobs_directory/000/19/working\ndebuggroup summary 0.13s command /usr/local/bin/circos -conf circos/conf/circos.conf -noparanoid\ndebuggroup summary 0.13s loading configuration from file circos/conf/circos.conf\ndebuggroup summary 0.13s found conf file circos/conf/circos.conf\ndebuggroup summary 0.23s debug will appear for these features: output,summary\ndebuggroup summary 0.23s bitmap output image ./circos.png\ndebuggroup summary 0.23s SVG output image ./circos.svg\ndebuggroup summary 0.23s parsing karyotype and organizing ideograms\ndebuggroup summary 0.24s karyotype has 2 chromosomes of total size 56,082\ndebuggroup summary 0.24s applying global and local scaling\ndebuggroup summary 0.24s allocating image, colors and brushes\ndebuggroup summary 4.78s drawing 2 ideograms of total size 56,082\ndebuggroup summary 4.78s drawing highlights and ideograms\ndebuggroup summary 4.82s found conf file /usr/local/bin/../etc/tracks/link.conf\ndebuggroup summary 4.82s process track_0 link circos/conf/../data/links-0.txt\ndebuggroup summary 4.83s drawing link track_0 z 0\ndebuggroup !circoswarning 4.86s Data point of type [link] [50000-50500] extended past end of ideogram [ctgA 0-50001]. This data point will be [trimmed].\ndebuggroup !circoswarning 4.86s Data point of type [link] [51000-51500] extended past end of ideogram [ctgA 0-50001]. This data point will be [hidden].\ndebuggroup summary 4.86s found conf file /usr/local/bin/../etc/tracks/histogram.conf\ndebuggroup summary 4.86s found conf file /usr/local/bin/../etc/tracks/scatter.conf\ndebuggroup summary 4.86s found conf file /usr/local/bin/../etc/tracks/tile.conf\ndebuggroup summary 4.86s processing track_0 histogram circos/conf/../data/data-0.txt\ndebuggroup summary 4.92s processing track_1 scatter circos/conf/../data/data-1.txt\ndebuggroup summary 5.04s processing track_2 tile circos/conf/../data/data-2.txt\ndebuggroup summary 5.05s drawing track_0 histogram z 0 data-0.txt orient out\ndebuggroup summary 5.06s found conf file /usr/local/bin/../etc/tracks/axis.conf\ndebuggroup summary 5.61s drawing track_1 scatter z 0 data-1.txt orient out\ndebuggroup summary 5.63s found conf file /usr/local/bin/../etc/tracks/axis.conf\ndebuggroup summary 5.78s drawing track_2 tile z 0 data-2.txt orient out\ndebuggroup summary 5.79s found conf file /usr/local/bin/../etc/tracks/axis.conf\ndebuggroup !circoswarning 5.92s Data point of type [tile] [3013-6130] extended past end of ideogram [ctgB 0-6079]. This data point will be [trimmed].\ndebuggroup output 5.93s generating output\ndebuggroup output 6.29s created PNG image ./circos.png (539 kb)\ndebuggroup output 6.30s created SVG image ./circos.svg (414 kb)\n", "stderr": "Use of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\nUse of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\nUse of uninitialized value within %Circos::Error::GROUPERROR in uc at /usr/local/bin/../lib/Circos/Error.pm line 354, line 21.\nUse of uninitialized value within %Circos::Error::GROUPERROR in uc at /usr/local/bin/../lib/Circos/Error.pm line 354, line 21.\nUse of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781, line 21.\nUse of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\nUse of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\nUse of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781, line 1214.\nUse of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\nUse of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.\nUse of uninitialized value within %Circos::Error::GROUPERROR in uc at /usr/local/bin/../lib/Circos/Error.pm line 354.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "10737", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "10737.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 18:36:38", "plugin": "core", "name": "start_epoch", "raw_value": "1725474998.0000000"}, {"title": "Job End Time", "value": "2024-09-04 18:36:45", "plugin": "core", "name": "end_epoch", "raw_value": "1725475005.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "7 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "7.0000000"}]}, "status": "success"}}, {"id": "deeptools_multi_bam_summary/3.3.2.0.0-0", "has_data": true, "data": {"tool_id": "deeptools_multi_bam_summary", "tool_version": "3.3.2.0.0", "test_index": 0, "time_seconds": 95.43912720680237, "inputs": {"multibam_conditional|bamfiles": [{"src": "hda", "id": "3cbec5b19229f469"}, {"src": "hda", "id": "3cbec5b19229f469"}], "mode|binSize": "10", "mode|modeOpt": "bins"}, "job": {"model_class": "Job", "id": "a0cf5e7e06f9f57f", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T18:31:38.022294", "update_time": "2024-09-04T18:32:36.517887", "galaxy_version": "24.1", "external_id": "gxy-kvv94", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/8/3/5/dataset_83569697-e414-40db-9ccb-d91cf668a609.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/9/1/b/metadata_91b79dcc-49a3-484a-ba6f-70faa2d287e8.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/8/3/5/dataset_83569697-e414-40db-9ccb-d91cf668a609.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/9/1/b/metadata_91b79dcc-49a3-484a-ba6f-70faa2d287e8.dat' './1.bam.bai' && multiBamSummary bins --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --outFileName '/galaxy/server/database/objects/6/1/c/dataset_61c664af-cfec-407f-a858-5a469b97cb00.dat' --bamfiles '0.bam' '1.bam' --labels 'bowtie2 test1.bam' 'bowtie2 test1.bam' --binSize '10' --distanceBetweenBins '0'", "user_email": "tests@fake.org", "command_version": "multiBamSummary 3.3.2", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "scalingFactors": "false", "outRawCounts": "false", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "region": "\"\"", "mode": "{\"__current_case__\": 0, \"binSize\": \"10\", \"distanceBetweenBins\": \"0\", \"modeOpt\": \"bins\"}", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibam_conditional": "{\"__current_case__\": 0, \"bamfiles\": {\"values\": [{\"id\": 1, \"src\": \"hda\"}, {\"id\": 1, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}"}, "inputs": {"multibam_conditional|bamfiles2": {"id": "3cbec5b19229f469", "src": "hda", "uuid": "83569697-e414-40db-9ccb-d91cf668a609"}, "multibam_conditional|bamfiles1": {"id": "3cbec5b19229f469", "src": "hda", "uuid": "83569697-e414-40db-9ccb-d91cf668a609"}, "multibam_conditional|bamfiles": {"id": "3cbec5b19229f469", "src": "hda", "uuid": "83569697-e414-40db-9ccb-d91cf668a609"}}, "outputs": {"outFile": {"id": "a0cf5e7e06f9f57f", "src": "hda", "uuid": "61c664af-cfec-407f-a858-5a469b97cb00"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of bins found: 1657\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Number of bins found: 1657\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-04 18:32:19", "plugin": "core", "name": "end_epoch", "raw_value": "1725474739.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 18:32:18", "plugin": "core", "name": "start_epoch", "raw_value": "1725474738.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "deeptools_multi_bam_summary/3.3.2.0.0-1", "has_data": true, "data": {"tool_id": "deeptools_multi_bam_summary", "tool_version": "3.3.2.0.0", "test_index": 1, "time_seconds": 25.80667996406555, "inputs": {"multibam_conditional|bamfiles": [{"src": "hda", "id": "2e44e9ff029c6820"}, {"src": "hda", "id": "2e44e9ff029c6820"}], "mode|region_file": {"src": "hda", "id": "7c84d18633e694f0"}, "mode|modeOpt": "BED-file"}, "job": {"model_class": "Job", "id": "25718ce0aef57e36", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0", "state": "error", "exit_code": null, "create_time": "2024-09-04T18:32:57.803959", "update_time": "2024-09-04T18:33:03.041702", "galaxy_version": "24.1", "external_id": "gxy-gjv5d", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/0/7/b/dataset_07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/2/6/4/metadata_2641dd70-609b-4f94-9c42-2b30489ecfa6.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/0/7/b/dataset_07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/2/6/4/metadata_2641dd70-609b-4f94-9c42-2b30489ecfa6.dat' './1.bam.bai' && multiBamSummary BED-file --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --outFileName '/galaxy/server/database/objects/5/f/5/dataset_5f516eee-0a8b-4a48-997f-5c7961be38d6.dat' --bamfiles '0.bam' '1.bam' --labels 'bowtie2 test1.bam' 'bowtie2 test1.bam' --BED /galaxy/server/database/objects/1/6/8/dataset_168b8377-1770-4dce-ba17-7aecf99d7738.dat", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "scalingFactors": "false", "outRawCounts": "false", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "region": "\"\"", "mode": "{\"__current_case__\": 1, \"modeOpt\": \"BED-file\", \"region_file\": {\"values\": [{\"id\": 4, \"src\": \"hda\"}]}}", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibam_conditional": "{\"__current_case__\": 0, \"bamfiles\": {\"values\": [{\"id\": 3, \"src\": \"hda\"}, {\"id\": 3, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}"}, "inputs": {"mode|region_file": {"id": "7c84d18633e694f0", "src": "hda", "uuid": "168b8377-1770-4dce-ba17-7aecf99d7738"}, "multibam_conditional|bamfiles2": {"id": "2e44e9ff029c6820", "src": "hda", "uuid": "07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9"}, "multibam_conditional|bamfiles1": {"id": "2e44e9ff029c6820", "src": "hda", "uuid": "07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9"}, "multibam_conditional|bamfiles": {"id": "2e44e9ff029c6820", "src": "hda", "uuid": "07b5eeaf-5a1b-4dc7-ade8-b80f34b1e0f9"}}, "outputs": {"outFile": {"id": "25718ce0aef57e36", "src": "hda", "uuid": "5f516eee-0a8b-4a48-997f-5c7961be38d6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of bins found: 3\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "Number of bins found: 3\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0, exit_code: None, stderr: Number of bins found: 3\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0, exit_code: None, stderr: Number of bins found: 3\n."], "status": "failure"}}, {"id": "diff/3.7+galaxy0-0", "has_data": true, "data": {"tool_id": "diff", "tool_version": "3.7+galaxy0", "test_index": 0, "time_seconds": 11.445114612579346, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "diff/3.7+galaxy0-1", "has_data": true, "data": {"tool_id": "diff", "tool_version": "3.7+galaxy0", "test_index": 1, "time_seconds": 36.14392852783203, "inputs": {"input1": {"src": "hda", "id": "7772ca923102aaaa"}, "input2": {"src": "hda", "id": "38b78b94c9753826"}, "generate_report": false}, "job": {"model_class": "Job", "id": "c6346922b0157d20", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0", "state": "ok", "exit_code": 1, "create_time": "2024-09-04T19:24:24.354513", "update_time": "2024-09-04T19:24:39.539111", "galaxy_version": "24.1", "external_id": "gxy-88dzb", "handler": null, "job_runner_name": null, "command_line": "diff -u '/galaxy/server/database/objects/7/e/0/dataset_7e0e5d24-9b41-494d-8d08-1a5a3b581fb3.dat' '/galaxy/server/database/objects/9/9/e/dataset_99e14ddb-c4b7-47ea-a078-ed729223f9d6.dat' > '/galaxy/server/database/objects/9/c/e/dataset_9ce2ef5b-2098-452e-947f-4ae9f302e1cd.dat';", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_format": "\"side-by-side\"", "generate_report": "false"}, "inputs": {"input1": {"id": "7772ca923102aaaa", "src": "hda", "uuid": "7e0e5d24-9b41-494d-8d08-1a5a3b581fb3"}, "input2": {"id": "38b78b94c9753826", "src": "hda", "uuid": "99e14ddb-c4b7-47ea-a078-ed729223f9d6"}}, "outputs": {"diff_file": {"id": "037787ea3e8909b9", "src": "hda", "uuid": "9ce2ef5b-2098-452e-947f-4ae9f302e1cd"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": 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"execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "diff/3.7+galaxy0-4", "has_data": true, "data": {"tool_id": "diff", "tool_version": "3.7+galaxy0", "test_index": 4, "time_seconds": 11.013369083404541, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "diff/3.7+galaxy0-5", "has_data": true, "data": {"tool_id": "diff", "tool_version": "3.7+galaxy0", "test_index": 5, "time_seconds": 32.124786376953125, "inputs": {"input1": {"src": "hda", "id": "994651ef8ae15d1e"}, "input2": {"src": "hda", "id": "994651ef8ae15d1e"}, "generate_report": true}, "job": {"model_class": "Job", "id": "1db26ca0a992cfa7", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:25:32.621087", "update_time": "2024-09-04T19:25:44.283438", "galaxy_version": "24.1", "external_id": "gxy-w24hc", "handler": null, "job_runner_name": null, "command_line": "diff -u '/galaxy/server/database/objects/4/f/c/dataset_4fc30241-efdf-44fe-92f1-0e7b7066ed88.dat' '/galaxy/server/database/objects/4/f/c/dataset_4fc30241-efdf-44fe-92f1-0e7b7066ed88.dat' > '/galaxy/server/database/objects/d/3/8/dataset_d3891ebd-6f09-45bf-beb2-e2391919d292.dat'; sed -e 's/@@title@@/Diff report for \"file 3.txt\" and \"file 3.txt\"/g' -e 's/@@outputformat@@/'side-by-side'/g' -e '/@@diffoutput@@/{r'/galaxy/server/database/objects/d/3/8/dataset_d3891ebd-6f09-45bf-beb2-e2391919d292.dat'' -e ';d}' '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/bgruening/diff/156d0908e232/diff/template.html' > '/galaxy/server/database/objects/2/9/6/dataset_2968d5e6-2430-446f-8a3e-8a95add16110.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_format": "\"side-by-side\"", "generate_report": "true"}, "inputs": {"input1": {"id": "994651ef8ae15d1e", "src": "hda", "uuid": "4fc30241-efdf-44fe-92f1-0e7b7066ed88"}, "input2": {"id": "994651ef8ae15d1e", "src": "hda", "uuid": "4fc30241-efdf-44fe-92f1-0e7b7066ed88"}}, "outputs": {"diff_file": {"id": "e5c773ba060c0b7f", "src": "hda", "uuid": "d3891ebd-6f09-45bf-beb2-e2391919d292"}, "html_file": {"id": "f0bae59a9fa83656", "src": "hda", "uuid": "2968d5e6-2430-446f-8a3e-8a95add16110"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-04 19:25:33", "plugin": "core", "name": "end_epoch", "raw_value": "1725477933.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:25:33", "plugin": "core", "name": "start_epoch", "raw_value": "1725477933.0000000"}, {"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": "fastq_paired_end_deinterlacer/1.1.5-0", "has_data": true, "data": {"tool_id": "fastq_paired_end_deinterlacer", "tool_version": "1.1.5", "test_index": 0, "time_seconds": 40.493459701538086, "inputs": {"input_file": {"src": "hda", "id": "5dce4c6ae032b20f"}}, "job": {"model_class": "Job", "id": "4c57e16f0544033d", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T18:33:23.682619", "update_time": "2024-09-04T18:33:41.693605", "galaxy_version": "24.1", "external_id": "gxy-4jsfb", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-paired-end-deinterlacer '/galaxy/server/database/objects/e/8/d/dataset_e8d7792b-afe1-46cd-9722-6d4ec0d04023.dat' 'sanger' '/galaxy/server/database/objects/1/d/6/dataset_1d6f386c-9764-4b55-ab5d-984e3eb5b578.dat' '/galaxy/server/database/objects/9/1/9/dataset_919f9a8b-68d3-45ab-a608-ed12440dede8.dat' '/galaxy/server/database/objects/c/c/7/dataset_cc7837f5-07ec-462b-a4b8-04a3677d1387.dat' '/galaxy/server/database/objects/7/2/1/dataset_721f4b3c-f62a-42e4-8ec2-e373f814c73e.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fastqsanger\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input_file": {"id": "5dce4c6ae032b20f", "src": "hda", "uuid": "e8d7792b-afe1-46cd-9722-6d4ec0d04023"}}, "outputs": {"output2_singles_file": {"id": "0ecf5896e74d14f4", "src": "hda", "uuid": "721f4b3c-f62a-42e4-8ec2-e373f814c73e"}, "output1_singles_file": {"id": "bc463e12e52d0ca9", "src": "hda", "uuid": "cc7837f5-07ec-462b-a4b8-04a3677d1387"}, "output2_pairs_file": {"id": "6cb2c6ca63395177", "src": "hda", "uuid": "919f9a8b-68d3-45ab-a608-ed12440dede8"}, "output1_pairs_file": {"id": "4c57e16f0544033d", "src": "hda", "uuid": "1d6f386c-9764-4b55-ab5d-984e3eb5b578"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "De-interlaced 5.0 pairs of sequences.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "De-interlaced 5.0 pairs of sequences.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-04 18:33:29", "plugin": "core", "name": "end_epoch", "raw_value": "1725474809.0000000"}, {"title": "Job Start Time", 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"\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastqsanger.gz\""}, "inputs": {"input_file": {"id": "11c24c9aadb92cb2", "src": "hda", "uuid": "ac0f347e-85db-4448-953a-7cce2b9cf79f"}}, "outputs": {"output2_singles_file": {"id": "6f075e09c4af720e", "src": "hda", "uuid": "854db4da-b44e-4eee-b8ea-62904c3251c4"}, "output1_singles_file": {"id": "e30beac5c8896cc4", "src": "hda", "uuid": "ce9dfdad-4ce4-4519-9832-bac112b2ed8a"}, "output2_pairs_file": {"id": "3bc05048bf9ac1a4", "src": "hda", "uuid": "e8e6ab20-1496-4456-9ec1-bed32081bb06"}, "output1_pairs_file": {"id": "d7567a01e2b6992a", "src": "hda", "uuid": "a211138a-5c91-40dc-acd0-ba72ec6d1c62"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "There were 2 reads with no mate.\nDe-interlaced 4.0 pairs of sequences.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "There were 2 reads with no mate.\nDe-interlaced 4.0 pairs of sequences.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-04 18:34:16", "plugin": "core", "name": "end_epoch", "raw_value": "1725474856.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 18:34:16", "plugin": "core", "name": "start_epoch", "raw_value": "1725474856.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastq_paired_end_deinterlacer/1.1.5-3", "has_data": true, "data": {"tool_id": "fastq_paired_end_deinterlacer", "tool_version": "1.1.5", "test_index": 3, "time_seconds": 35.82276940345764, "inputs": {"input_file": {"src": "hda", "id": "9152fd457868d13a"}}, "job": {"model_class": "Job", "id": "11c24c9aadb92cb2", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T18:34:50.759835", "update_time": "2024-09-04T18:35:03.718780", "galaxy_version": "24.1", "external_id": "gxy-xvxh6", "handler": null, "job_runner_name": null, "command_line": "gx-fastq-paired-end-deinterlacer '/galaxy/server/database/objects/e/5/c/dataset_e5c936d9-fd11-4a2f-828e-87174913f7ac.dat' 'sanger.bz2' '/galaxy/server/database/objects/e/7/5/dataset_e750e255-fdd9-472a-b401-e5d0287b7e28.dat' '/galaxy/server/database/objects/7/9/7/dataset_7973cf50-b3cf-44d4-8c7d-541b9e2bf4ce.dat' '/galaxy/server/database/objects/d/4/7/dataset_d47dc877-d4e2-4078-b1ff-9e97462fbd4d.dat' '/galaxy/server/database/objects/6/b/d/dataset_6bd4c4b8-8452-42b4-8b8e-7e80f44dc2e5.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fastqsanger.bz2\""}, "inputs": {"input_file": {"id": "9152fd457868d13a", "src": "hda", "uuid": "e5c936d9-fd11-4a2f-828e-87174913f7ac"}}, "outputs": {"output1_pairs_file": {"id": "6c407653984b74eb", "src": "hda", "uuid": "e750e255-fdd9-472a-b401-e5d0287b7e28"}, "output2_pairs_file": {"id": "6906245fd4fc934f", "src": "hda", "uuid": "7973cf50-b3cf-44d4-8c7d-541b9e2bf4ce"}, "output1_singles_file": {"id": "4f77978a9b4252f1", "src": "hda", "uuid": "d47dc877-d4e2-4078-b1ff-9e97462fbd4d"}, "output2_singles_file": {"id": "fc7e83e9d90a8ab5", "src": "hda", "uuid": "6bd4c4b8-8452-42b4-8b8e-7e80f44dc2e5"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "There were 2 reads with no mate.\nDe-interlaced 4.0 pairs of sequences.\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "There were 2 reads with no mate.\nDe-interlaced 4.0 pairs of sequences.\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-04 18:34:52", "plugin": "core", "name": "end_epoch", "raw_value": "1725474892.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 18:34:52", "plugin": "core", "name": "start_epoch", "raw_value": "1725474892.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "ivar_trim/1.2.2+galaxy1-0", "has_data": true, "data": {"tool_id": "ivar_trim", "tool_version": "1.2.2+galaxy1", "test_index": 0, "time_seconds": 43.40780830383301, "inputs": {"input_bam": {"src": "hda", "id": "eb20477a98551d6c"}, "primer|input_bed": {"src": "hda", "id": "c6f05526bc24899b"}, "inc_primers": true}, "job": {"model_class": "Job", "id": "4da5680171e847fa", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:30:00.986061", "update_time": "2024-09-04T19:30:21.151319", "galaxy_version": "24.1", "external_id": "gxy-txlbp", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/9/e/e/dataset_9eee8747-6a96-4a6d-bb4b-d280659563db.dat' bed.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/db536ad45f28/ivar_trim/sanitize_bed.py' bed.bed && ln -s '/galaxy/server/database/objects/7/5/3/dataset_75392a27-d342-4574-941d-c14e30b7a6b3.dat' sorted.bam && ln -s '/galaxy/server/database/objects/_metadata_files/b/e/1/metadata_be1860ee-7279-44c7-8ac4-867b53f47319.dat' sorted.bam.bai && ivar trim -i sorted.bam -b bed.bed -m 30 -q 20 -s 4 -e -p trimmed && samtools sort -@ ${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam", "user_email": "tests@fake.org", "command_version": "iVar version 1.2.2", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "inc_primers": "true", "window_width": "\"4\"", "min_qual": "\"20\"", "min_len": "\"30\"", "primer": "{\"__current_case__\": 0, \"input_bed\": {\"values\": [{\"id\": 278, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"input_bam": {"id": "eb20477a98551d6c", "src": "hda", "uuid": "75392a27-d342-4574-941d-c14e30b7a6b3"}, "primer|input_bed": {"id": "c6f05526bc24899b", "src": "hda", "uuid": "9eee8747-6a96-4a6d-bb4b-d280659563db"}}, "outputs": {"output_bam": {"id": "5ede65662f937a67", "src": "hda", "uuid": "c0fc7bc1-1796-4a84-9b57-96651bb391e0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Found 196 primers in BED file\n\nNumber of references in file: 1\nNC_045512.2\nUsing Region: NC_045512.2\n\nFound 51688 mapped reads\nFound 0 unmapped reads\nSorted By Coordinate\n-------\nProcessed 10% reads ... \nProcessed 20% reads ... \nProcessed 30% reads ... \nProcessed 40% reads ... \nProcessed 50% reads ... \nProcessed 60% reads ... \nProcessed 70% reads ... \nProcessed 80% reads ... \nProcessed 90% reads ... \nProcessed 100% reads ... \n\n-------\nResults: \nPrimer Name\tRead Count\nnCoV-2019_1_LEFT\t15\nnCoV-2019_1_RIGHT\t5\nnCoV-2019_2_LEFT\t9\nnCoV-2019_2_RIGHT\t11\nnCoV-2019_3_LEFT\t14\nnCoV-2019_3_RIGHT\t18\nnCoV-2019_4_LEFT\t13\nnCoV-2019_4_RIGHT\t2\nnCoV-2019_5_LEFT\t2\nnCoV-2019_5_RIGHT\t8\nnCoV-2019_6_LEFT\t10\nnCoV-2019_6_RIGHT\t6\nnCoV-2019_7_LEFT\t15\nnCoV-2019_7_RIGHT\t8\nnCoV-2019_8_LEFT\t3\nnCoV-2019_8_RIGHT\t6\nnCoV-2019_9_LEFT\t13\nnCoV-2019_9_RIGHT\t7\nnCoV-2019_10_LEFT\t13\nnCoV-2019_10_RIGHT\t7\nnCoV-2019_11_LEFT\t10\nnCoV-2019_11_RIGHT\t19\nnCoV-2019_12_LEFT\t27\nnCoV-2019_12_RIGHT\t5\nnCoV-2019_13_LEFT\t17\nnCoV-2019_13_RIGHT\t37\nnCoV-2019_14_LEFT\t33\nnCoV-2019_14_RIGHT\t56\nnCoV-2019_15_LEFT\t43\nnCoV-2019_15_RIGHT\t39\nnCoV-2019_16_LEFT\t113\nnCoV-2019_16_RIGHT\t58\nnCoV-2019_17_LEFT\t67\nnCoV-2019_17_RIGHT\t12\nnCoV-2019_18_LEFT\t11\nnCoV-2019_18_RIGHT\t24\nnCoV-2019_19_LEFT\t47\nnCoV-2019_19_RIGHT\t27\nnCoV-2019_20_LEFT\t18\nnCoV-2019_20_RIGHT\t31\nnCoV-2019_21_LEFT\t77\nnCoV-2019_21_RIGHT\t16\nnCoV-2019_22_LEFT\t36\nnCoV-2019_22_RIGHT\t34\nnCoV-2019_23_LEFT\t24\nnCoV-2019_23_RIGHT\t1\nnCoV-2019_24_LEFT\t11\nnCoV-2019_24_RIGHT\t4\nnCoV-2019_25_LEFT\t4\nnCoV-2019_25_RIGHT\t6\nnCoV-2019_26_LEFT\t7\nnCoV-2019_26_RIGHT\t8\nnCoV-2019_27_LEFT\t49\nnCoV-2019_27_RIGHT\t17\nnCoV-2019_28_LEFT\t9\nnCoV-2019_28_RIGHT\t4\nnCoV-2019_29_LEFT\t3\nnCoV-2019_29_RIGHT\t46\nnCoV-2019_30_LEFT\t6\nnCoV-2019_30_RIGHT\t16\nnCoV-2019_31_LEFT\t22\nnCoV-2019_31_RIGHT\t45\nnCoV-2019_32_LEFT\t73\nnCoV-2019_32_RIGHT\t30\nnCoV-2019_33_LEFT\t13\nnCoV-2019_33_RIGHT\t24\nnCoV-2019_34_LEFT\t31\nnCoV-2019_34_RIGHT\t27\nnCoV-2019_35_LEFT\t26\nnCoV-2019_35_RIGHT\t56\nnCoV-2019_36_LEFT\t72\nnCoV-2019_36_RIGHT\t89\nnCoV-2019_37_LEFT\t45\nnCoV-2019_37_RIGHT\t100\nnCoV-2019_38_LEFT\t108\nnCoV-2019_38_RIGHT\t65\nnCoV-2019_39_LEFT\t58\nnCoV-2019_39_RIGHT\t27\nnCoV-2019_40_LEFT\t40\nnCoV-2019_40_RIGHT\t11\nnCoV-2019_41_LEFT\t19\nnCoV-2019_41_RIGHT\t3\nnCoV-2019_42_LEFT\t26\nnCoV-2019_42_RIGHT\t54\nnCoV-2019_43_LEFT\t30\nnCoV-2019_43_RIGHT\t12\nnCoV-2019_44_LEFT\t30\nnCoV-2019_44_RIGHT\t49\nnCoV-2019_45_LEFT\t30\nnCoV-2019_45_RIGHT\t13\nnCoV-2019_46_LEFT\t9\nnCoV-2019_46_RIGHT\t25\nnCoV-2019_47_LEFT\t18\nnCoV-2019_47_RIGHT\t15\nnCoV-2019_48_LEFT\t42\nnCoV-2019_48_RIGHT\t26\nnCoV-2019_49_LEFT\t23\nnCoV-2019_49_RIGHT\t30\nnCoV-2019_50_LEFT\t15\nnCoV-2019_50_RIGHT\t11\nnCoV-2019_51_LEFT\t47\nnCoV-2019_51_RIGHT\t30\nnCoV-2019_52_LEFT\t17\nnCoV-2019_52_RIGHT\t16\nnCoV-2019_53_LEFT\t49\nnCoV-2019_53_RIGHT\t23\nnCoV-2019_54_LEFT\t23\nnCoV-2019_54_RIGHT\t8\nnCoV-2019_55_LEFT\t41\nnCoV-2019_55_RIGHT\t56\nnCoV-2019_56_LEFT\t25\nnCoV-2019_56_RIGHT\t42\nnCoV-2019_57_LEFT\t72\nnCoV-2019_57_RIGHT\t53\nnCoV-2019_58_LEFT\t9\nnCoV-2019_58_RIGHT\t4\nnCoV-2019_59_LEFT\t23\nnCoV-2019_59_RIGHT\t13\nnCoV-2019_60_LEFT\t11\nnCoV-2019_60_RIGHT\t10\nnCoV-2019_61_LEFT\t21\nnCoV-2019_61_RIGHT\t19\nnCoV-2019_62_LEFT\t10\nnCoV-2019_62_RIGHT\t8\nnCoV-2019_63_LEFT\t30\nnCoV-2019_63_RIGHT\t20\nnCoV-2019_64_LEFT\t3\nnCoV-2019_64_RIGHT\t4\nnCoV-2019_65_LEFT\t4\nnCoV-2019_65_RIGHT\t36\nnCoV-2019_66_LEFT\t16\nnCoV-2019_66_RIGHT\t1\nnCoV-2019_67_LEFT\t3\nnCoV-2019_67_RIGHT\t0\nnCoV-2019_68_LEFT\t5\nnCoV-2019_68_RIGHT\t5\nnCoV-2019_69_LEFT\t10\nnCoV-2019_69_RIGHT\t3\nnCoV-2019_70_LEFT\t0\nnCoV-2019_70_RIGHT\t1\nnCoV-2019_71_LEFT\t1\nnCoV-2019_71_RIGHT\t2\nnCoV-2019_72_LEFT\t3\nnCoV-2019_72_RIGHT\t2\nnCoV-2019_73_LEFT\t0\nnCoV-2019_73_RIGHT\t2\nnCoV-2019_74_LEFT\t0\nnCoV-2019_74_RIGHT\t0\nnCoV-2019_75_LEFT\t1\nnCoV-2019_75_RIGHT\t1\nnCoV-2019_76_LEFT\t1\nnCoV-2019_76_RIGHT\t7\nnCoV-2019_77_LEFT\t16\nnCoV-2019_77_RIGHT\t57\nnCoV-2019_78_LEFT\t41\nnCoV-2019_78_RIGHT\t14\nnCoV-2019_79_LEFT\t2\nnCoV-2019_79_RIGHT\t10\nnCoV-2019_80_LEFT\t56\nnCoV-2019_80_RIGHT\t22\nnCoV-2019_81_LEFT\t18\nnCoV-2019_81_RIGHT\t48\nnCoV-2019_82_LEFT\t97\nnCoV-2019_82_RIGHT\t29\nnCoV-2019_83_LEFT\t14\nnCoV-2019_83_RIGHT\t26\nnCoV-2019_84_LEFT\t25\nnCoV-2019_84_RIGHT\t32\nnCoV-2019_85_LEFT\t40\nnCoV-2019_85_RIGHT\t20\nnCoV-2019_86_LEFT\t30\nnCoV-2019_86_RIGHT\t24\nnCoV-2019_87_LEFT\t28\nnCoV-2019_87_RIGHT\t2\nnCoV-2019_88_LEFT\t39\nnCoV-2019_88_RIGHT\t57\nnCoV-2019_89_LEFT\t22\nnCoV-2019_89_RIGHT\t19\nnCoV-2019_90_LEFT\t15\nnCoV-2019_90_RIGHT\t13\nnCoV-2019_91_LEFT\t15\nnCoV-2019_91_RIGHT\t1\nnCoV-2019_92_LEFT\t6\nnCoV-2019_92_RIGHT\t8\nnCoV-2019_93_LEFT\t23\nnCoV-2019_93_RIGHT\t16\nnCoV-2019_94_LEFT\t83\nnCoV-2019_94_RIGHT\t32\nnCoV-2019_95_LEFT\t20\nnCoV-2019_95_RIGHT\t7\nnCoV-2019_96_LEFT\t13\nnCoV-2019_96_RIGHT\t11\nnCoV-2019_97_LEFT\t0\nnCoV-2019_97_RIGHT\t1\nnCoV-2019_98_LEFT\t2\nnCoV-2019_98_RIGHT\t1\n\nTrimmed primers from 8.79% (4545) of reads.\n3.14% (1623) of reads were quality trimmed below the minimum length of 30 bp and were not writen to file.\n88.58% (45784) of reads started outside of primer regions. Since the -e flag was given, these reads were written to file.\n", "tool_stderr": "[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "Found 196 primers in BED file\n\nNumber of references in file: 1\nNC_045512.2\nUsing Region: NC_045512.2\n\nFound 51688 mapped reads\nFound 0 unmapped reads\nSorted By Coordinate\n-------\nProcessed 10% reads ... \nProcessed 20% reads ... \nProcessed 30% reads ... \nProcessed 40% reads ... \nProcessed 50% reads ... \nProcessed 60% reads ... \nProcessed 70% reads ... \nProcessed 80% reads ... \nProcessed 90% reads ... \nProcessed 100% reads ... \n\n-------\nResults: \nPrimer Name\tRead Count\nnCoV-2019_1_LEFT\t15\nnCoV-2019_1_RIGHT\t5\nnCoV-2019_2_LEFT\t9\nnCoV-2019_2_RIGHT\t11\nnCoV-2019_3_LEFT\t14\nnCoV-2019_3_RIGHT\t18\nnCoV-2019_4_LEFT\t13\nnCoV-2019_4_RIGHT\t2\nnCoV-2019_5_LEFT\t2\nnCoV-2019_5_RIGHT\t8\nnCoV-2019_6_LEFT\t10\nnCoV-2019_6_RIGHT\t6\nnCoV-2019_7_LEFT\t15\nnCoV-2019_7_RIGHT\t8\nnCoV-2019_8_LEFT\t3\nnCoV-2019_8_RIGHT\t6\nnCoV-2019_9_LEFT\t13\nnCoV-2019_9_RIGHT\t7\nnCoV-2019_10_LEFT\t13\nnCoV-2019_10_RIGHT\t7\nnCoV-2019_11_LEFT\t10\nnCoV-2019_11_RIGHT\t19\nnCoV-2019_12_LEFT\t27\nnCoV-2019_12_RIGHT\t5\nnCoV-2019_13_LEFT\t17\nnCoV-2019_13_RIGHT\t37\nnCoV-2019_14_LEFT\t33\nnCoV-2019_14_RIGHT\t56\nnCoV-2019_15_LEFT\t43\nnCoV-2019_15_RIGHT\t39\nnCoV-2019_16_LEFT\t113\nnCoV-2019_16_RIGHT\t58\nnCoV-2019_17_LEFT\t67\nnCoV-2019_17_RIGHT\t12\nnCoV-2019_18_LEFT\t11\nnCoV-2019_18_RIGHT\t24\nnCoV-2019_19_LEFT\t47\nnCoV-2019_19_RIGHT\t27\nnCoV-2019_20_LEFT\t18\nnCoV-2019_20_RIGHT\t31\nnCoV-2019_21_LEFT\t77\nnCoV-2019_21_RIGHT\t16\nnCoV-2019_22_LEFT\t36\nnCoV-2019_22_RIGHT\t34\nnCoV-2019_23_LEFT\t24\nnCoV-2019_23_RIGHT\t1\nnCoV-2019_24_LEFT\t11\nnCoV-2019_24_RIGHT\t4\nnCoV-2019_25_LEFT\t4\nnCoV-2019_25_RIGHT\t6\nnCoV-2019_26_LEFT\t7\nnCoV-2019_26_RIGHT\t8\nnCoV-2019_27_LEFT\t49\nnCoV-2019_27_RIGHT\t17\nnCoV-2019_28_LEFT\t9\nnCoV-2019_28_RIGHT\t4\nnCoV-2019_29_LEFT\t3\nnCoV-2019_29_RIGHT\t46\nnCoV-2019_30_LEFT\t6\nnCoV-2019_30_RIGHT\t16\nnCoV-2019_31_LEFT\t22\nnCoV-2019_31_RIGHT\t45\nnCoV-2019_32_LEFT\t73\nnCoV-2019_32_RIGHT\t30\nnCoV-2019_33_LEFT\t13\nnCoV-2019_33_RIGHT\t24\nnCoV-2019_34_LEFT\t31\nnCoV-2019_34_RIGHT\t27\nnCoV-2019_35_LEFT\t26\nnCoV-2019_35_RIGHT\t56\nnCoV-2019_36_LEFT\t72\nnCoV-2019_36_RIGHT\t89\nnCoV-2019_37_LEFT\t45\nnCoV-2019_37_RIGHT\t100\nnCoV-2019_38_LEFT\t108\nnCoV-2019_38_RIGHT\t65\nnCoV-2019_39_LEFT\t58\nnCoV-2019_39_RIGHT\t27\nnCoV-2019_40_LEFT\t40\nnCoV-2019_40_RIGHT\t11\nnCoV-2019_41_LEFT\t19\nnCoV-2019_41_RIGHT\t3\nnCoV-2019_42_LEFT\t26\nnCoV-2019_42_RIGHT\t54\nnCoV-2019_43_LEFT\t30\nnCoV-2019_43_RIGHT\t12\nnCoV-2019_44_LEFT\t30\nnCoV-2019_44_RIGHT\t49\nnCoV-2019_45_LEFT\t30\nnCoV-2019_45_RIGHT\t13\nnCoV-2019_46_LEFT\t9\nnCoV-2019_46_RIGHT\t25\nnCoV-2019_47_LEFT\t18\nnCoV-2019_47_RIGHT\t15\nnCoV-2019_48_LEFT\t42\nnCoV-2019_48_RIGHT\t26\nnCoV-2019_49_LEFT\t23\nnCoV-2019_49_RIGHT\t30\nnCoV-2019_50_LEFT\t15\nnCoV-2019_50_RIGHT\t11\nnCoV-2019_51_LEFT\t47\nnCoV-2019_51_RIGHT\t30\nnCoV-2019_52_LEFT\t17\nnCoV-2019_52_RIGHT\t16\nnCoV-2019_53_LEFT\t49\nnCoV-2019_53_RIGHT\t23\nnCoV-2019_54_LEFT\t23\nnCoV-2019_54_RIGHT\t8\nnCoV-2019_55_LEFT\t41\nnCoV-2019_55_RIGHT\t56\nnCoV-2019_56_LEFT\t25\nnCoV-2019_56_RIGHT\t42\nnCoV-2019_57_LEFT\t72\nnCoV-2019_57_RIGHT\t53\nnCoV-2019_58_LEFT\t9\nnCoV-2019_58_RIGHT\t4\nnCoV-2019_59_LEFT\t23\nnCoV-2019_59_RIGHT\t13\nnCoV-2019_60_LEFT\t11\nnCoV-2019_60_RIGHT\t10\nnCoV-2019_61_LEFT\t21\nnCoV-2019_61_RIGHT\t19\nnCoV-2019_62_LEFT\t10\nnCoV-2019_62_RIGHT\t8\nnCoV-2019_63_LEFT\t30\nnCoV-2019_63_RIGHT\t20\nnCoV-2019_64_LEFT\t3\nnCoV-2019_64_RIGHT\t4\nnCoV-2019_65_LEFT\t4\nnCoV-2019_65_RIGHT\t36\nnCoV-2019_66_LEFT\t16\nnCoV-2019_66_RIGHT\t1\nnCoV-2019_67_LEFT\t3\nnCoV-2019_67_RIGHT\t0\nnCoV-2019_68_LEFT\t5\nnCoV-2019_68_RIGHT\t5\nnCoV-2019_69_LEFT\t10\nnCoV-2019_69_RIGHT\t3\nnCoV-2019_70_LEFT\t0\nnCoV-2019_70_RIGHT\t1\nnCoV-2019_71_LEFT\t1\nnCoV-2019_71_RIGHT\t2\nnCoV-2019_72_LEFT\t3\nnCoV-2019_72_RIGHT\t2\nnCoV-2019_73_LEFT\t0\nnCoV-2019_73_RIGHT\t2\nnCoV-2019_74_LEFT\t0\nnCoV-2019_74_RIGHT\t0\nnCoV-2019_75_LEFT\t1\nnCoV-2019_75_RIGHT\t1\nnCoV-2019_76_LEFT\t1\nnCoV-2019_76_RIGHT\t7\nnCoV-2019_77_LEFT\t16\nnCoV-2019_77_RIGHT\t57\nnCoV-2019_78_LEFT\t41\nnCoV-2019_78_RIGHT\t14\nnCoV-2019_79_LEFT\t2\nnCoV-2019_79_RIGHT\t10\nnCoV-2019_80_LEFT\t56\nnCoV-2019_80_RIGHT\t22\nnCoV-2019_81_LEFT\t18\nnCoV-2019_81_RIGHT\t48\nnCoV-2019_82_LEFT\t97\nnCoV-2019_82_RIGHT\t29\nnCoV-2019_83_LEFT\t14\nnCoV-2019_83_RIGHT\t26\nnCoV-2019_84_LEFT\t25\nnCoV-2019_84_RIGHT\t32\nnCoV-2019_85_LEFT\t40\nnCoV-2019_85_RIGHT\t20\nnCoV-2019_86_LEFT\t30\nnCoV-2019_86_RIGHT\t24\nnCoV-2019_87_LEFT\t28\nnCoV-2019_87_RIGHT\t2\nnCoV-2019_88_LEFT\t39\nnCoV-2019_88_RIGHT\t57\nnCoV-2019_89_LEFT\t22\nnCoV-2019_89_RIGHT\t19\nnCoV-2019_90_LEFT\t15\nnCoV-2019_90_RIGHT\t13\nnCoV-2019_91_LEFT\t15\nnCoV-2019_91_RIGHT\t1\nnCoV-2019_92_LEFT\t6\nnCoV-2019_92_RIGHT\t8\nnCoV-2019_93_LEFT\t23\nnCoV-2019_93_RIGHT\t16\nnCoV-2019_94_LEFT\t83\nnCoV-2019_94_RIGHT\t32\nnCoV-2019_95_LEFT\t20\nnCoV-2019_95_RIGHT\t7\nnCoV-2019_96_LEFT\t13\nnCoV-2019_96_RIGHT\t11\nnCoV-2019_97_LEFT\t0\nnCoV-2019_97_RIGHT\t1\nnCoV-2019_98_LEFT\t2\nnCoV-2019_98_RIGHT\t1\n\nTrimmed primers from 8.79% (4545) of reads.\n3.14% (1623) of reads were quality trimmed below the minimum length of 30 bp and were not writen to file.\n88.58% (45784) of reads started outside of primer regions. Since the -e flag was given, these reads were written to file.\n", "stderr": "[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:30:09", "plugin": "core", "name": "end_epoch", "raw_value": "1725478209.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:30:08", "plugin": "core", "name": "start_epoch", "raw_value": "1725478208.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "ivar_trim/1.2.2+galaxy1-1", "has_data": true, "data": {"tool_id": "ivar_trim", "tool_version": "1.2.2+galaxy1", "test_index": 1, "time_seconds": 48.93506717681885, "inputs": {"input_bam": {"src": "hda", "id": "3fca84e75f451602"}, "primer|input_bed": {"src": "hda", "id": "2c06cd51ac5caf5f"}, "inc_primers": true}, "job": {"model_class": "Job", "id": "a009eef793f954c9", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:30:44.441154", "update_time": "2024-09-04T19:31:09.626938", "galaxy_version": "24.1", "external_id": "gxy-cvcb2", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/0/b/7/dataset_0b78d828-e768-4c2c-bd4d-58eaa242a1e5.dat' bed.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/db536ad45f28/ivar_trim/sanitize_bed.py' bed.bed && ln -s '/galaxy/server/database/objects/3/c/e/dataset_3ce1704a-1956-49bc-81be-a826e3ecac50.dat' sorted.bam && ln -s '/galaxy/server/database/objects/_metadata_files/b/5/d/metadata_b5d4cba3-5097-49e9-b374-189ae006418b.dat' sorted.bam.bai && ivar trim -i sorted.bam -b bed.bed -m 30 -q 20 -s 4 -e -p trimmed && samtools sort -@ ${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam", "user_email": "tests@fake.org", "command_version": "iVar version 1.2.2", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "inc_primers": "true", "window_width": "\"4\"", "min_qual": "\"20\"", "min_len": "\"30\"", "primer": "{\"__current_case__\": 0, \"input_bed\": {\"values\": [{\"id\": 282, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"input_bam": {"id": "3fca84e75f451602", "src": "hda", "uuid": "3ce1704a-1956-49bc-81be-a826e3ecac50"}, "primer|input_bed": {"id": "ffd3f31d9b1abc47", "src": "hda", "uuid": "0b78d828-e768-4c2c-bd4d-58eaa242a1e5"}}, "outputs": {"output_bam": {"id": "8701e815a2b008de", "src": "hda", "uuid": "491db6e4-4378-4129-9a18-c0a5b4257d38"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Found 196 primers in BED file\n\nNumber of references in file: 1\nNC_045512.2\nUsing Region: NC_045512.2\n\nFound 51688 mapped reads\nFound 0 unmapped reads\nSorted By Coordinate\n-------\nProcessed 10% reads ... \nProcessed 20% reads ... \nProcessed 30% reads ... \nProcessed 40% reads ... \nProcessed 50% reads ... \nProcessed 60% reads ... \nProcessed 70% reads ... \nProcessed 80% reads ... \nProcessed 90% reads ... \nProcessed 100% reads ... \n\n-------\nResults: \nPrimer Name\tRead Count\nregion_0\t15\nregion_1\t5\nregion_2\t9\nregion_3\t11\nregion_4\t14\nregion_5\t18\nregion_6\t13\nregion_7\t2\nregion_8\t2\nregion_9\t8\nregion_10\t10\nregion_11\t6\nregion_12\t15\nregion_13\t8\nregion_14\t3\nregion_15\t6\nregion_16\t13\nregion_17\t7\nregion_18\t13\nregion_19\t7\nregion_20\t10\nregion_21\t19\nregion_22\t27\nregion_23\t5\nregion_24\t17\nregion_25\t37\nregion_26\t33\nregion_27\t56\nregion_28\t43\nregion_29\t39\nregion_30\t113\nregion_31\t58\nregion_32\t67\nregion_33\t12\nregion_34\t11\nregion_35\t24\nregion_36\t47\nregion_37\t27\nregion_38\t18\nregion_39\t31\nregion_40\t77\nregion_41\t16\nregion_42\t36\nregion_43\t34\nregion_44\t24\nregion_45\t1\nregion_46\t11\nregion_47\t4\nregion_48\t4\nregion_49\t6\nregion_50\t7\nregion_51\t8\nregion_52\t49\nregion_53\t17\nregion_54\t9\nregion_55\t4\nregion_56\t3\nregion_57\t46\nregion_58\t6\nregion_59\t16\nregion_60\t22\nregion_61\t45\nregion_62\t73\nregion_63\t30\nregion_64\t13\nregion_65\t24\nregion_66\t31\nregion_67\t27\nregion_68\t26\nregion_69\t56\nregion_70\t72\nregion_71\t89\nregion_72\t45\nregion_73\t100\nregion_74\t108\nregion_75\t65\nregion_76\t58\nregion_77\t27\nregion_78\t40\nregion_79\t11\nregion_80\t19\nregion_81\t3\nregion_82\t26\nregion_83\t54\nregion_84\t30\nregion_85\t12\nregion_86\t30\nregion_87\t49\nregion_88\t30\nregion_89\t13\nregion_90\t9\nregion_91\t25\nregion_92\t18\nregion_93\t15\nregion_94\t42\nregion_95\t26\nregion_96\t23\nregion_97\t30\nregion_98\t15\nregion_99\t11\nregion_100\t47\nregion_101\t30\nregion_102\t17\nregion_103\t16\nregion_104\t49\nregion_105\t23\nregion_106\t23\nregion_107\t8\nregion_108\t41\nregion_109\t56\nregion_110\t25\nregion_111\t42\nregion_112\t72\nregion_113\t53\nregion_114\t9\nregion_115\t4\nregion_116\t23\nregion_117\t13\nregion_118\t11\nregion_119\t10\nregion_120\t21\nregion_121\t19\nregion_122\t10\nregion_123\t8\nregion_124\t30\nregion_125\t20\nregion_126\t3\nregion_127\t4\nregion_128\t4\nregion_129\t36\nregion_130\t16\nregion_131\t1\nregion_132\t3\nregion_133\t0\nregion_134\t5\nregion_135\t5\nregion_136\t10\nregion_137\t3\nregion_138\t0\nregion_139\t1\nregion_140\t1\nregion_141\t2\nregion_142\t3\nregion_143\t2\nregion_144\t0\nregion_145\t2\nregion_146\t0\nregion_147\t0\nregion_148\t1\nregion_149\t1\nregion_150\t1\nregion_151\t7\nregion_152\t16\nregion_153\t57\nregion_154\t41\nregion_155\t14\nregion_156\t2\nregion_157\t10\nregion_158\t56\nregion_159\t22\nregion_160\t18\nregion_161\t48\nregion_162\t97\nregion_163\t29\nregion_164\t14\nregion_165\t26\nregion_166\t25\nregion_167\t32\nregion_168\t40\nregion_169\t20\nregion_170\t30\nregion_171\t24\nregion_172\t28\nregion_173\t2\nregion_174\t39\nregion_175\t57\nregion_176\t22\nregion_177\t19\nregion_178\t15\nregion_179\t13\nregion_180\t15\nregion_181\t1\nregion_182\t6\nregion_183\t8\nregion_184\t23\nregion_185\t16\nregion_186\t83\nregion_187\t32\nregion_188\t20\nregion_189\t7\nregion_190\t13\nregion_191\t11\nregion_192\t0\nregion_193\t1\nregion_194\t2\nregion_195\t1\n\nTrimmed primers from 8.79% (4545) of reads.\n3.14% (1623) of reads were quality trimmed below the minimum length of 30 bp and were not writen to file.\n88.58% (45784) of reads started outside of primer regions. Since the -e flag was given, these reads were written to file.\n", "tool_stderr": "[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "Found 196 primers in BED file\n\nNumber of references in file: 1\nNC_045512.2\nUsing Region: NC_045512.2\n\nFound 51688 mapped reads\nFound 0 unmapped reads\nSorted By Coordinate\n-------\nProcessed 10% reads ... \nProcessed 20% reads ... \nProcessed 30% reads ... \nProcessed 40% reads ... \nProcessed 50% reads ... \nProcessed 60% reads ... \nProcessed 70% reads ... \nProcessed 80% reads ... \nProcessed 90% reads ... \nProcessed 100% reads ... \n\n-------\nResults: \nPrimer Name\tRead Count\nregion_0\t15\nregion_1\t5\nregion_2\t9\nregion_3\t11\nregion_4\t14\nregion_5\t18\nregion_6\t13\nregion_7\t2\nregion_8\t2\nregion_9\t8\nregion_10\t10\nregion_11\t6\nregion_12\t15\nregion_13\t8\nregion_14\t3\nregion_15\t6\nregion_16\t13\nregion_17\t7\nregion_18\t13\nregion_19\t7\nregion_20\t10\nregion_21\t19\nregion_22\t27\nregion_23\t5\nregion_24\t17\nregion_25\t37\nregion_26\t33\nregion_27\t56\nregion_28\t43\nregion_29\t39\nregion_30\t113\nregion_31\t58\nregion_32\t67\nregion_33\t12\nregion_34\t11\nregion_35\t24\nregion_36\t47\nregion_37\t27\nregion_38\t18\nregion_39\t31\nregion_40\t77\nregion_41\t16\nregion_42\t36\nregion_43\t34\nregion_44\t24\nregion_45\t1\nregion_46\t11\nregion_47\t4\nregion_48\t4\nregion_49\t6\nregion_50\t7\nregion_51\t8\nregion_52\t49\nregion_53\t17\nregion_54\t9\nregion_55\t4\nregion_56\t3\nregion_57\t46\nregion_58\t6\nregion_59\t16\nregion_60\t22\nregion_61\t45\nregion_62\t73\nregion_63\t30\nregion_64\t13\nregion_65\t24\nregion_66\t31\nregion_67\t27\nregion_68\t26\nregion_69\t56\nregion_70\t72\nregion_71\t89\nregion_72\t45\nregion_73\t100\nregion_74\t108\nregion_75\t65\nregion_76\t58\nregion_77\t27\nregion_78\t40\nregion_79\t11\nregion_80\t19\nregion_81\t3\nregion_82\t26\nregion_83\t54\nregion_84\t30\nregion_85\t12\nregion_86\t30\nregion_87\t49\nregion_88\t30\nregion_89\t13\nregion_90\t9\nregion_91\t25\nregion_92\t18\nregion_93\t15\nregion_94\t42\nregion_95\t26\nregion_96\t23\nregion_97\t30\nregion_98\t15\nregion_99\t11\nregion_100\t47\nregion_101\t30\nregion_102\t17\nregion_103\t16\nregion_104\t49\nregion_105\t23\nregion_106\t23\nregion_107\t8\nregion_108\t41\nregion_109\t56\nregion_110\t25\nregion_111\t42\nregion_112\t72\nregion_113\t53\nregion_114\t9\nregion_115\t4\nregion_116\t23\nregion_117\t13\nregion_118\t11\nregion_119\t10\nregion_120\t21\nregion_121\t19\nregion_122\t10\nregion_123\t8\nregion_124\t30\nregion_125\t20\nregion_126\t3\nregion_127\t4\nregion_128\t4\nregion_129\t36\nregion_130\t16\nregion_131\t1\nregion_132\t3\nregion_133\t0\nregion_134\t5\nregion_135\t5\nregion_136\t10\nregion_137\t3\nregion_138\t0\nregion_139\t1\nregion_140\t1\nregion_141\t2\nregion_142\t3\nregion_143\t2\nregion_144\t0\nregion_145\t2\nregion_146\t0\nregion_147\t0\nregion_148\t1\nregion_149\t1\nregion_150\t1\nregion_151\t7\nregion_152\t16\nregion_153\t57\nregion_154\t41\nregion_155\t14\nregion_156\t2\nregion_157\t10\nregion_158\t56\nregion_159\t22\nregion_160\t18\nregion_161\t48\nregion_162\t97\nregion_163\t29\nregion_164\t14\nregion_165\t26\nregion_166\t25\nregion_167\t32\nregion_168\t40\nregion_169\t20\nregion_170\t30\nregion_171\t24\nregion_172\t28\nregion_173\t2\nregion_174\t39\nregion_175\t57\nregion_176\t22\nregion_177\t19\nregion_178\t15\nregion_179\t13\nregion_180\t15\nregion_181\t1\nregion_182\t6\nregion_183\t8\nregion_184\t23\nregion_185\t16\nregion_186\t83\nregion_187\t32\nregion_188\t20\nregion_189\t7\nregion_190\t13\nregion_191\t11\nregion_192\t0\nregion_193\t1\nregion_194\t2\nregion_195\t1\n\nTrimmed primers from 8.79% (4545) of reads.\n3.14% (1623) of reads were quality trimmed below the minimum length of 30 bp and were not writen to file.\n88.58% (45784) of reads started outside of primer regions. Since the -e flag was given, these reads were written to file.\n", "stderr": "[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:30:59", "plugin": "core", "name": "end_epoch", "raw_value": "1725478259.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:30:58", "plugin": "core", "name": "start_epoch", "raw_value": "1725478258.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "ivar_trim/1.2.2+galaxy1-2", "has_data": true, "data": {"tool_id": "ivar_trim", "tool_version": "1.2.2+galaxy1", "test_index": 2, "time_seconds": 36.64368653297424, "inputs": {"input_bam": {"src": "hda", "id": "118fe02616a2a888"}, "primer|input_bed": {"src": "hda", "id": "733b56c7858705e9"}, "primer|source": "history"}, "job": {"model_class": "Job", "id": "6b5e034ca1871913", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:31:33.342341", "update_time": "2024-09-04T19:31:46.399410", "galaxy_version": "24.1", "external_id": "gxy-zrb45", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/e/f/d/dataset_efd7befd-d3bf-466b-bd15-a198ab046bed.dat' bed.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/db536ad45f28/ivar_trim/sanitize_bed.py' bed.bed && ln -s '/galaxy/server/database/objects/b/f/6/dataset_bf6fbcc0-1a80-433c-a9b0-249b844a38db.dat' sorted.bam && ln -s '/galaxy/server/database/objects/_metadata_files/a/3/7/metadata_a378a7d2-d9cf-486d-a474-8fe946e5cbfe.dat' sorted.bam.bai && ivar trim -i sorted.bam -b bed.bed -m 30 -q 20 -s 4 -p trimmed && samtools sort -@ ${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam", "user_email": "tests@fake.org", "command_version": "iVar version 1.2.2", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "inc_primers": "false", "window_width": "\"4\"", "min_qual": "\"20\"", "min_len": "\"30\"", "primer": "{\"__current_case__\": 0, \"input_bed\": {\"values\": [{\"id\": 285, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"input_bam": {"id": "118fe02616a2a888", "src": "hda", "uuid": "bf6fbcc0-1a80-433c-a9b0-249b844a38db"}, "primer|input_bed": {"id": "733b56c7858705e9", "src": "hda", "uuid": "efd7befd-d3bf-466b-bd15-a198ab046bed"}}, "outputs": {"output_bam": {"id": "d2143dac54e2f1db", "src": "hda", "uuid": "0d4f9487-668f-430b-8251-8db3e487a1db"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Found 68 primers in BED file\n\nNumber of references in file: 1\nPRV\nUsing Region: PRV\n\nFound 32550 mapped reads\nFound 0 unmapped reads\nSorted By Coordinate\n-------\nProcessed 10% reads ... \nProcessed 20% reads ... \nProcessed 30% reads ... \nProcessed 40% reads ... \nProcessed 50% reads ... \nProcessed 60% reads ... \nProcessed 70% reads ... \nProcessed 80% reads ... \nProcessed 90% reads ... \nProcessed 100% reads ... \n\n-------\nResults: \nPrimer Name\tRead Count\n400_1_out_R\t116\n400_2_out_L\t265\n400_2_out_R\t269\n400_3_out_L*\t47\n400_3_out_R*\t55\n400_4_out_L\t118\n400_4_out_R\t119\n400_5_out_L\t1078\n400_5_out_R\t1043\n400_6_out_L\t139\n400_6_out_R\t140\n400_7_out_L\t246\n400_7_out_R\t251\n400_8_out_L*\t164\n400_8_out_R*\t164\n400_9_out_L*\t103\n400_9_out_R*\t104\n400_10_out_L\t358\n400_10_out_R\t358\n400_11_out_L\t1538\n400_11_out_R\t1539\n400_12_out_L\t295\n400_12_out_R\t293\n400_13_out_L\t209\n400_13_out_R\t229\n400_14_out_L*\t736\n400_14_out_R*\t735\n400_15_out_L\t87\n400_15_out_R\t82\n400_16_out_L*\t498\n400_16_out_R*\t493\n400_17_out_L**\t1420\n400_17_out_R**\t1414\n400_18_out_L**\t9\n400_18_out_R**\t9\n400_19_out_L\t43\n400_19_out_R\t50\n400_20_out_L*\t2128\n400_20_out_R*\t2158\n400_21_out_L*\t15\n400_21_out_R*\t10\n400_22_out_L**\t33\n400_22_out_R**\t5\n400_23_out_L\t179\n400_23_out_R\t169\n400_24_out_L**\t80\n400_24_out_R**\t80\n400_25_out_L**\t3035\n400_25_out_R**\t3064\n400_26_out_L\t420\n400_26_out_R\t423\n400_27_out_L\t68\n400_27_out_R\t6\n400_28_out_L\t41\n400_28_out_R\t43\n400_29_out_L\t113\n400_29_out_R\t117\n400_30_out_L\t1057\n400_30_out_R\t1054\n400_31_out_L\t165\n400_31_out_R\t170\n400_32_out_L\t277\n400_32_out_R\t282\n400_33_out_L*\t436\n400_33_out_R*\t433\n400_34_out_L*\t688\n400_34_out_R*\t688\n400_35_out_L\t0\n\nTrimmed primers from 99.09% (32253) of reads.\n10.66% (3469) of reads were quality trimmed below the minimum length of 30 bp and were not writen to file.\n0.8% (261) of reads that started outside of primer regions were not written to file.\n", "tool_stderr": "[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "Found 68 primers in BED file\n\nNumber of references in file: 1\nPRV\nUsing Region: PRV\n\nFound 32550 mapped reads\nFound 0 unmapped reads\nSorted By Coordinate\n-------\nProcessed 10% reads ... \nProcessed 20% reads ... \nProcessed 30% reads ... \nProcessed 40% reads ... \nProcessed 50% reads ... \nProcessed 60% reads ... \nProcessed 70% reads ... \nProcessed 80% reads ... \nProcessed 90% reads ... \nProcessed 100% reads ... \n\n-------\nResults: \nPrimer Name\tRead Count\n400_1_out_R\t116\n400_2_out_L\t265\n400_2_out_R\t269\n400_3_out_L*\t47\n400_3_out_R*\t55\n400_4_out_L\t118\n400_4_out_R\t119\n400_5_out_L\t1078\n400_5_out_R\t1043\n400_6_out_L\t139\n400_6_out_R\t140\n400_7_out_L\t246\n400_7_out_R\t251\n400_8_out_L*\t164\n400_8_out_R*\t164\n400_9_out_L*\t103\n400_9_out_R*\t104\n400_10_out_L\t358\n400_10_out_R\t358\n400_11_out_L\t1538\n400_11_out_R\t1539\n400_12_out_L\t295\n400_12_out_R\t293\n400_13_out_L\t209\n400_13_out_R\t229\n400_14_out_L*\t736\n400_14_out_R*\t735\n400_15_out_L\t87\n400_15_out_R\t82\n400_16_out_L*\t498\n400_16_out_R*\t493\n400_17_out_L**\t1420\n400_17_out_R**\t1414\n400_18_out_L**\t9\n400_18_out_R**\t9\n400_19_out_L\t43\n400_19_out_R\t50\n400_20_out_L*\t2128\n400_20_out_R*\t2158\n400_21_out_L*\t15\n400_21_out_R*\t10\n400_22_out_L**\t33\n400_22_out_R**\t5\n400_23_out_L\t179\n400_23_out_R\t169\n400_24_out_L**\t80\n400_24_out_R**\t80\n400_25_out_L**\t3035\n400_25_out_R**\t3064\n400_26_out_L\t420\n400_26_out_R\t423\n400_27_out_L\t68\n400_27_out_R\t6\n400_28_out_L\t41\n400_28_out_R\t43\n400_29_out_L\t113\n400_29_out_R\t117\n400_30_out_L\t1057\n400_30_out_R\t1054\n400_31_out_L\t165\n400_31_out_R\t170\n400_32_out_L\t277\n400_32_out_R\t282\n400_33_out_L*\t436\n400_33_out_R*\t433\n400_34_out_L*\t688\n400_34_out_R*\t688\n400_35_out_L\t0\n\nTrimmed primers from 99.09% (32253) of reads.\n10.66% (3469) of reads were quality trimmed below the minimum length of 30 bp and were not writen to file.\n0.8% (261) of reads that started outside of primer regions were not written to file.\n", "stderr": "[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:31:36", "plugin": "core", "name": "end_epoch", "raw_value": "1725478296.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:31:35", "plugin": "core", "name": "start_epoch", "raw_value": "1725478295.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "ivar_trim/1.2.2+galaxy1-3", "has_data": true, "data": {"tool_id": "ivar_trim", "tool_version": "1.2.2+galaxy1", "test_index": 3, "time_seconds": 59.286391735076904, "inputs": {"input_bam": {"src": "hda", "id": "3646f2182036416c"}, "primer|input_bed": {"src": "hda", "id": "d4faaef0b5991d8d"}, "primer|source": "history"}, "job": {"model_class": "Job", "id": "91ad96a2a528808c", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.2.2+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:32:10.659830", "update_time": "2024-09-04T19:32:46.224740", "galaxy_version": "24.1", "external_id": "gxy-md76s", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/3/b/3/dataset_3b397c2b-d885-43c4-8bfd-bbe86727534c.dat' bed.bed && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/db536ad45f28/ivar_trim/sanitize_bed.py' bed.bed && ln -s '/galaxy/server/database/objects/9/7/5/dataset_975e75b7-3a76-4beb-84ed-97d8013de938.dat' sorted.bam && ln -s '/galaxy/server/database/objects/_metadata_files/d/a/f/metadata_daf2c3ad-ed3b-476e-97e5-ec8167494ff9.dat' sorted.bam.bai && ivar trim -i sorted.bam -b bed.bed -m 30 -q 20 -s 4 -p trimmed && samtools sort -@ ${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam", "user_email": "tests@fake.org", "command_version": "iVar version 1.2.2", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "inc_primers": "false", "window_width": "\"4\"", "min_qual": "\"20\"", "min_len": "\"30\"", "primer": "{\"__current_case__\": 0, \"input_bed\": {\"values\": [{\"id\": 288, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"input_bam": {"id": "3646f2182036416c", "src": "hda", "uuid": "975e75b7-3a76-4beb-84ed-97d8013de938"}, "primer|input_bed": {"id": "d4faaef0b5991d8d", "src": "hda", "uuid": "3b397c2b-d885-43c4-8bfd-bbe86727534c"}}, "outputs": {"output_bam": {"id": "4f9ce3d182d7f6d9", "src": "hda", "uuid": "a68a849c-abae-405e-8841-d397aec6bf86"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Found 68 primers in BED file\n\nNumber of references in file: 1\nPRV\nUsing Region: PRV\n\nFound 40964 mapped reads\nFound 0 unmapped reads\nSorted By Coordinate\n-------\nProcessed 10% reads ... \nProcessed 20% reads ... \nProcessed 30% reads ... \nProcessed 40% reads ... \nProcessed 50% reads ... \nProcessed 60% reads ... \nProcessed 70% reads ... \nProcessed 80% reads ... \nProcessed 90% reads ... \nProcessed 100% reads ... \n\n-------\nResults: \nPrimer Name\tRead Count\n400_1_out_R\t156\n400_2_out_L\t227\n400_2_out_R\t238\n400_3_out_L*\t76\n400_3_out_R*\t76\n400_4_out_L\t91\n400_4_out_R\t95\n400_5_out_L\t1544\n400_5_out_R\t1541\n400_6_out_L\t37\n400_6_out_R\t38\n400_7_out_L\t540\n400_7_out_R\t538\n400_8_out_L*\t143\n400_8_out_R*\t143\n400_9_out_L*\t90\n400_9_out_R*\t93\n400_10_out_L\t400\n400_10_out_R\t400\n400_11_out_L\t2536\n400_11_out_R\t2534\n400_12_out_L\t144\n400_12_out_R\t141\n400_13_out_L\t298\n400_13_out_R\t307\n400_14_out_L*\t676\n400_14_out_R*\t671\n400_15_out_L\t183\n400_15_out_R\t180\n400_16_out_L*\t419\n400_16_out_R*\t417\n400_17_out_L**\t2321\n400_17_out_R**\t2315\n400_18_out_L**\t32\n400_18_out_R**\t6\n400_19_out_L\t67\n400_19_out_R\t69\n400_20_out_L*\t1653\n400_20_out_R*\t1681\n400_21_out_L*\t15\n400_21_out_R*\t13\n400_22_out_L**\t17\n400_22_out_R**\t2\n400_23_out_L\t297\n400_23_out_R\t292\n400_24_out_L**\t61\n400_24_out_R**\t67\n400_25_out_L**\t4360\n400_25_out_R**\t4378\n400_26_out_L\t308\n400_26_out_R\t303\n400_27_out_L\t69\n400_27_out_R\t21\n400_28_out_L\t17\n400_28_out_R\t17\n400_29_out_L\t185\n400_29_out_R\t187\n400_30_out_L\t1512\n400_30_out_R\t1510\n400_31_out_L\t265\n400_31_out_R\t273\n400_32_out_L\t411\n400_32_out_R\t411\n400_33_out_L*\t545\n400_33_out_R*\t536\n400_34_out_L*\t699\n400_34_out_R*\t699\n400_35_out_L\t0\n\nTrimmed primers from 99.08% (40586) of reads.\n10.83% (4435) of reads were quality trimmed below the minimum length of 30 bp and were not writen to file.\n0.84% (344) of reads that started outside of primer regions were not written to file.\n", "tool_stderr": "[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_stdout": "", "job_stderr": "", "stdout": "Found 68 primers in BED file\n\nNumber of references in file: 1\nPRV\nUsing Region: PRV\n\nFound 40964 mapped reads\nFound 0 unmapped reads\nSorted By Coordinate\n-------\nProcessed 10% reads ... \nProcessed 20% reads ... \nProcessed 30% reads ... \nProcessed 40% reads ... \nProcessed 50% reads ... \nProcessed 60% reads ... \nProcessed 70% reads ... \nProcessed 80% reads ... \nProcessed 90% reads ... \nProcessed 100% reads ... \n\n-------\nResults: \nPrimer Name\tRead Count\n400_1_out_R\t156\n400_2_out_L\t227\n400_2_out_R\t238\n400_3_out_L*\t76\n400_3_out_R*\t76\n400_4_out_L\t91\n400_4_out_R\t95\n400_5_out_L\t1544\n400_5_out_R\t1541\n400_6_out_L\t37\n400_6_out_R\t38\n400_7_out_L\t540\n400_7_out_R\t538\n400_8_out_L*\t143\n400_8_out_R*\t143\n400_9_out_L*\t90\n400_9_out_R*\t93\n400_10_out_L\t400\n400_10_out_R\t400\n400_11_out_L\t2536\n400_11_out_R\t2534\n400_12_out_L\t144\n400_12_out_R\t141\n400_13_out_L\t298\n400_13_out_R\t307\n400_14_out_L*\t676\n400_14_out_R*\t671\n400_15_out_L\t183\n400_15_out_R\t180\n400_16_out_L*\t419\n400_16_out_R*\t417\n400_17_out_L**\t2321\n400_17_out_R**\t2315\n400_18_out_L**\t32\n400_18_out_R**\t6\n400_19_out_L\t67\n400_19_out_R\t69\n400_20_out_L*\t1653\n400_20_out_R*\t1681\n400_21_out_L*\t15\n400_21_out_R*\t13\n400_22_out_L**\t17\n400_22_out_R**\t2\n400_23_out_L\t297\n400_23_out_R\t292\n400_24_out_L**\t61\n400_24_out_R**\t67\n400_25_out_L**\t4360\n400_25_out_R**\t4378\n400_26_out_L\t308\n400_26_out_R\t303\n400_27_out_L\t69\n400_27_out_R\t21\n400_28_out_L\t17\n400_28_out_R\t17\n400_29_out_L\t185\n400_29_out_R\t187\n400_30_out_L\t1512\n400_30_out_R\t1510\n400_31_out_L\t265\n400_31_out_R\t273\n400_32_out_L\t411\n400_32_out_R\t411\n400_33_out_L*\t545\n400_33_out_R*\t536\n400_34_out_L*\t699\n400_34_out_R*\t699\n400_35_out_L\t0\n\nTrimmed primers from 99.08% (40586) of reads.\n10.83% (4435) of reads were quality trimmed below the minimum length of 30 bp and were not writen to file.\n0.84% (344) of reads that started outside of primer regions were not written to file.\n", "stderr": "[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:32:35", "plugin": "core", "name": "end_epoch", "raw_value": "1725478355.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:32:34", "plugin": "core", "name": "start_epoch", "raw_value": "1725478354.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "ivar_trim/1.2.2+galaxy1-4", "has_data": true, "data": {"tool_id": "ivar_trim", "tool_version": "1.2.2+galaxy1", "test_index": 4, "status": "skip"}}, {"id": "limma_voom/3.50.1+galaxy0-0", "has_data": true, "data": {"tool_id": "limma_voom", "tool_version": "3.50.1+galaxy0", "test_index": 0, "time_seconds": 73.49820637702942, "inputs": {"input|counts": {"src": "hda", "id": "377d84736949d9d5"}, "input|fact|rep_factor_0|factorName": "Genotype", "input|fact|rep_factor_0|groupNames": "Mut,Mut,Mut,WT,WT,WT", "input|format": "matrix", "cont|rep_contrast_0|contrast": "Mut-WT", "cont|rep_contrast_1|contrast": "WT-Mut", "cont|cfile": "no", "adv|topgenes": "6", "adv|normalisationOption": "TMM"}, "job": {"model_class": "Job", "id": "3352612fbd760959", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T18:40:52.857894", "update_time": "2024-09-04T18:41:46.512524", "galaxy_version": "24.1", "external_id": "gxy-kcv7m", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/d6f5fa4ee473/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/0/6/d/dataset_06d10672-7b83-472c-817f-f90adc40a6e1.dat' -o '/galaxy/server/database/objects/0/6/d/dataset_06d10672-7b83-472c-817f-f90adc40a6e1_files' -m '/galaxy/server/database/objects/9/b/1/dataset_9b14c529-7be8-4337-ba95-e307b72808ce.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -D 'Mut-WT,WT-Mut' -P i -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/0/6/d/dataset_06d10672-7b83-472c-817f-f90adc40a6e1_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/0/6/d/dataset_06d10672-7b83-472c-817f-f90adc40a6e1_files'", "user_email": "tests@fake.org", "command_version": "R version 4.1.2 (2021-11-01) -- \"Bird Hippie\", limma version 3.50.1, edgeR version 3.36.0, statmod version 1.4.36, scales version 1.1.1, rjson version 0.2.21, getopt version 1.20.3, gplots version 3.1.1, Glimma version 2.4.0", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"lfc\": \"0.0\", \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true, \"topgenes\": \"6\", \"treat\": false}", "out": "{\"filtCounts\": false, \"libinfo\": false, \"normCounts\": false, \"plots\": \"i\", \"rdaOption\": false, \"rscript\": false}", "f": "{\"filt\": {\"__current_case__\": 1, \"filt_select\": \"no\"}}", "cont": "{\"__current_case__\": 1, \"cfile\": \"no\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": \"Mut-WT\"}, {\"__index__\": 1, \"contrast\": \"WT-Mut\"}]}", "anno": "{\"__current_case__\": 1, \"annoOpt\": \"no\"}", "input": "{\"__current_case__\": 1, \"counts\": {\"values\": [{\"id\": 47, \"src\": \"hda\"}]}, \"fact\": {\"__current_case__\": 1, \"ffile\": \"no\", \"rep_factor\": [{\"__index__\": 0, \"factorName\": \"Genotype\", \"groupNames\": \"Mut,Mut,Mut,WT,WT,WT\"}]}, \"format\": \"matrix\"}", "deMethod": "{\"__current_case__\": 0, \"de_select\": \"voom\", \"weightOption\": false}"}, "inputs": {"input|counts": {"id": "377d84736949d9d5", "src": "hda", "uuid": "9b14c529-7be8-4337-ba95-e307b72808ce"}}, "outputs": {"outReport": {"id": "737c9dcbc9781406", "src": "hda", "uuid": "06d10672-7b83-472c-817f-f90adc40a6e1"}, "__new_primary_file_outTables|limma-voom_Mut-WT__": {"id": "6d0cdac37f748553", "src": "hda", "uuid": "f21316a3-3322-444c-8e45-c332e9efd6d4"}, "__new_primary_file_outTables|limma-voom_WT-Mut__": {"id": "c66cb77c577757d0", "src": "hda", "uuid": "d2dab25c-14b4-47be-a394-6fbfb5c3aae0"}}, "copied_from_job_id": null, "output_collections": {"outTables": {"src": "hdca", "id": "3cbec5b19229f469"}}, "tool_stdout": "[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[1] \"Extracting counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 18:41:10", "plugin": "core", "name": "start_epoch", "raw_value": "1725475270.0000000"}, {"title": "Job End Time", "value": "2024-09-04 18:41:29", "plugin": "core", 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\"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true, \"topgenes\": \"6\", \"treat\": false}", "out": "{\"filtCounts\": false, \"libinfo\": false, \"normCounts\": false, \"plots\": \"i\", \"rdaOption\": false, \"rscript\": false}", "f": "{\"filt\": {\"__current_case__\": 1, \"filt_select\": \"no\"}}", "cont": "{\"__current_case__\": 1, \"cfile\": \"no\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": \"Mut-WT\"}]}", "anno": "{\"__current_case__\": 1, \"annoOpt\": \"no\"}", "input": "{\"__current_case__\": 1, \"counts\": {\"values\": [{\"id\": 116, \"src\": \"hda\"}]}, \"fact\": {\"__current_case__\": 1, \"ffile\": \"no\", \"rep_factor\": [{\"__index__\": 0, \"factorName\": \"Genotype\", \"groupNames\": \"Mut,Mut,Mut,WT,WT,WT\"}, {\"__index__\": 1, \"factorName\": \"Batch\", \"groupNames\": \"b1,b2,b3,b1,b2,b3\"}]}, \"format\": \"matrix\"}", "deMethod": "{\"__current_case__\": 0, \"de_select\": \"voom\", \"weightOption\": false}"}, 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DE results\"\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "19 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "19.0000000"}, {"title": "Job End Time", "value": "2024-09-04 18:53:52", "plugin": "core", "name": "end_epoch", "raw_value": "1725476032.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 18:53:33", "plugin": "core", "name": "start_epoch", "raw_value": "1725476013.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "limma_voom/3.50.1+galaxy0-4", "has_data": true, "data": {"tool_id": "limma_voom", "tool_version": "3.50.1+galaxy0", "test_index": 4, "time_seconds": 18.61949896812439, "execution_problem": "Input staging problem: Job in error state.. 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"job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "19 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "19.0000000"}, {"title": "Job End Time", "value": "2024-09-04 18:45:17", "plugin": "core", "name": "end_epoch", "raw_value": "1725475517.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 18:44:58", "plugin": "core", "name": "start_epoch", "raw_value": "1725475498.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "limma_voom/3.50.1+galaxy0-5", "has_data": true, "data": {"tool_id": "limma_voom", "tool_version": "3.50.1+galaxy0", "test_index": 5, "time_seconds": 50.90337538719177, "inputs": {"input|counts": {"src": "hda", "id": "7cc3a8eed359160a"}, "input|fact|rep_factor_0|factorName": "Genotype", "input|fact|rep_factor_0|groupNames": "Mut,Mut,Mut,WT,WT,WT", "input|format": "matrix", "cont|rep_contrast_0|contrast": "Mut-WT", "cont|cfile": "no", "f|filt|cformat|cntReq": "10", "f|filt|cformat|samples|cntSampleReq": "3", "f|filt|cformat|samples|count_select": "sample", "f|filt|cformat|format_select": "counts", "f|filt|filt_select": "yes", "out|filtCounts": true, "out|normCounts": true, "adv|topgenes": "6", "adv|normalisationOption": "TMM"}, "job": {"model_class": "Job", "id": "8d7146d47ef91171", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T18:55:17.596625", "update_time": "2024-09-04T18:55:47.480373", "galaxy_version": "24.1", "external_id": "gxy-p8n7v", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/d6f5fa4ee473/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/f/9/d/dataset_f9d5984c-599b-48dc-a63b-bf9265da480b.dat' -o '/galaxy/server/database/objects/f/9/d/dataset_f9d5984c-599b-48dc-a63b-bf9265da480b_files' -m '/galaxy/server/database/objects/2/9/9/dataset_2998dbe2-3bb5-4a1b-be96-cbbe27180d86.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT' -D 'Mut-WT' -z '10' -s '3' -P i -F -x -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/f/9/d/dataset_f9d5984c-599b-48dc-a63b-bf9265da480b_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/f/9/d/dataset_f9d5984c-599b-48dc-a63b-bf9265da480b_files' && cp '/galaxy/server/database/objects/f/9/d/dataset_f9d5984c-599b-48dc-a63b-bf9265da480b_files'/*counts output_dir/", "user_email": "tests@fake.org", "command_version": "R version 4.1.2 (2021-11-01) -- \"Bird Hippie\", limma version 3.50.1, edgeR version 3.36.0, statmod version 1.4.36, scales version 1.1.1, rjson version 0.2.21, getopt version 1.20.3, gplots version 3.1.1, Glimma version 2.4.0", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"lfc\": \"0.0\", \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true, \"topgenes\": \"6\", \"treat\": false}", "out": "{\"filtCounts\": true, \"libinfo\": false, \"normCounts\": true, \"plots\": \"i\", \"rdaOption\": false, \"rscript\": false}", "f": "{\"filt\": {\"__current_case__\": 0, \"cformat\": {\"__current_case__\": 1, \"cntReq\": \"10\", \"format_select\": \"counts\", \"samples\": {\"__current_case__\": 1, \"cntSampleReq\": \"3\", \"count_select\": \"sample\"}}, \"filt_select\": \"yes\"}}", "cont": "{\"__current_case__\": 1, \"cfile\": \"no\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": \"Mut-WT\"}]}", "anno": "{\"__current_case__\": 1, \"annoOpt\": \"no\"}", "input": "{\"__current_case__\": 1, \"counts\": {\"values\": [{\"id\": 123, \"src\": \"hda\"}]}, \"fact\": {\"__current_case__\": 1, \"ffile\": \"no\", \"rep_factor\": [{\"__index__\": 0, \"factorName\": \"Genotype\", \"groupNames\": \"Mut,Mut,Mut,WT,WT,WT\"}]}, \"format\": \"matrix\"}", "deMethod": "{\"__current_case__\": 0, \"de_select\": \"voom\", \"weightOption\": false}"}, "inputs": {"input|counts": {"id": "7cc3a8eed359160a", "src": "hda", "uuid": "2998dbe2-3bb5-4a1b-be96-cbbe27180d86"}}, "outputs": {"outReport": {"id": "abf37687bf9608f2", "src": "hda", "uuid": "f9d5984c-599b-48dc-a63b-bf9265da480b"}, "outFilt": {"id": "e8b877bd15532157", "src": "hda", "uuid": "6a6e1c51-e554-48d9-8764-0e0b8937a23f"}, "outNorm": {"id": "0a3f0440f0ce50ae", "src": "hda", "uuid": "113e4da1-0f3a-4743-b382-96b3a3369964"}, "__new_primary_file_outTables|limma-voom_Mut-WT__": {"id": "e6f1ae45bfadd061", "src": "hda", "uuid": "09e4924e-5142-4a90-aa83-6d6e022de70f"}}, "copied_from_job_id": null, "output_collections": {"outTables": {"src": "hdca", "id": "6f075e09c4af720e"}}, "tool_stdout": "[1] \"Extracting counts\"\n[1] \"Outputting filtered counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[1] \"Extracting counts\"\n[1] \"Outputting filtered counts\"\n[1] \"Generating DGEList object\"\n[1] \"Generating Design\"\n[1] \"Calculating Normalisation Factors\"\n[1] \"Generating Contrasts\"\n[1] \"Generating MDS plot\"\n[1] \"Generating DE results\"\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "19 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "19.0000000"}, {"title": "Job End Time", "value": "2024-09-04 18:55:37", "plugin": "core", "name": "end_epoch", "raw_value": "1725476137.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 18:55:18", "plugin": 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"toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T18:46:35.627584", "update_time": "2024-09-04T18:47:07.616093", "galaxy_version": "24.1", "external_id": "gxy-69hwt", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/d6f5fa4ee473/limma_voom/limma_voom.R' -R '/galaxy/server/database/objects/1/b/9/dataset_1b9e4f21-0906-471e-99a0-538ef787e0ef.dat' -o '/galaxy/server/database/objects/1/b/9/dataset_1b9e4f21-0906-471e-99a0-538ef787e0ef_files' -j '[[\"Genotype\", [{\"Mut\": [\"/galaxy/server/database/objects/c/0/b/dataset_c0b62c38-24f6-443c-acb3-3454a28bc6c0.dat\", \"/galaxy/server/database/objects/f/6/f/dataset_f6ff0766-c438-4eaf-891b-7ac5dead4887.dat\", \"/galaxy/server/database/objects/0/1/7/dataset_0172193e-b68b-40b6-bb67-bf3994a19df4.dat\"]}, {\"WT\": [\"/galaxy/server/database/objects/c/2/2/dataset_c22c131c-bf4a-41cd-8a63-a6b3a005d678.dat\", \"/galaxy/server/database/objects/d/3/5/dataset_d35fef90-5cb8-4347-8565-cc85b8fc945d.dat\", \"/galaxy/server/database/objects/2/a/d/dataset_2ad7439e-3934-4f28-b196-066b4f20185f.dat\"]}]], [\"Batch\", [{\"b3\": [\"/galaxy/server/database/objects/2/a/d/dataset_2ad7439e-3934-4f28-b196-066b4f20185f.dat\", \"/galaxy/server/database/objects/0/1/7/dataset_0172193e-b68b-40b6-bb67-bf3994a19df4.dat\"]}, {\"b2\": [\"/galaxy/server/database/objects/d/3/5/dataset_d35fef90-5cb8-4347-8565-cc85b8fc945d.dat\", \"/galaxy/server/database/objects/f/6/f/dataset_f6ff0766-c438-4eaf-891b-7ac5dead4887.dat\"]}, {\"b1\": [\"/galaxy/server/database/objects/c/2/2/dataset_c22c131c-bf4a-41cd-8a63-a6b3a005d678.dat\", \"/galaxy/server/database/objects/c/0/b/dataset_c0b62c38-24f6-443c-acb3-3454a28bc6c0.dat\"]}]]]' -a '/galaxy/server/database/objects/c/b/a/dataset_cba9188a-52dc-410d-9a7e-75ee90e31393.dat' -D 'Mut-WT,WT-Mut' -P i -x -l '0.0' -p '0.05' -d 'BH' -G '6' -n 'TMM' -b && mkdir ./output_dir && cp '/galaxy/server/database/objects/1/b/9/dataset_1b9e4f21-0906-471e-99a0-538ef787e0ef_files'/*tsv output_dir/ && cp -r ./glimma* '/galaxy/server/database/objects/1/b/9/dataset_1b9e4f21-0906-471e-99a0-538ef787e0ef_files' && cp '/galaxy/server/database/objects/1/b/9/dataset_1b9e4f21-0906-471e-99a0-538ef787e0ef_files'/*counts output_dir/", "user_email": "tests@fake.org", "command_version": "R version 4.1.2 (2021-11-01) -- \"Bird Hippie\", limma version 3.50.1, edgeR version 3.36.0, statmod version 1.4.36, scales version 1.1.1, rjson version 0.2.21, getopt version 1.20.3, gplots version 3.1.1, Glimma version 2.4.0", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"lfc\": \"0.0\", \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true, \"topgenes\": \"6\", \"treat\": false}", "out": 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"toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-09-04T18:37:21.127148", "update_time": "2024-09-04T18:37:47.806755", "galaxy_version": "24.1", "external_id": "gxy-j5jbq", "handler": null, "job_runner_name": null, "command_line": "mummer -l '20' -b -threads ${GALAXY_SLOTS:-1} -qthreads ${GALAXY_SLOTS:-1} '/galaxy/server/database/objects/5/c/7/dataset_5c778596-6f7c-4484-a34c-c1d1f1d62b82.dat' '/galaxy/server/database/objects/7/6/b/dataset_76bbb1a6-c800-4cf0-8e9e-71c76ff5ed94.dat' > '/galaxy/server/database/objects/7/1/1/dataset_71196343-4536-4f57-ba54-12b66aeecaf3.dat' && mummerplot -b '20' -s 'small' -terminal png -title 'Title' '/galaxy/server/database/objects/7/1/1/dataset_71196343-4536-4f57-ba54-12b66aeecaf3.dat' && gnuplot < out.gp", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "mumplot": "{\"__current_case__\": 0, \"breaklen\": \"20\", \"color\": \"\", \"coverage\": \"\", \"fat\": false, \"filter\": false, \"labels\": {\"IDs\": \"no\", \"__current_case__\": 1}, \"plot\": \"yes\", \"range\": {\"__current_case__\": 1, \"custom\": \"no\"}, \"size\": \"small\", \"snp\": false, \"title\": \"Title\"}", "options": "{\"__current_case__\": 1, \"advanced\": \"defaults\"}", "position": "false", "substring": "false", "print_length": "false", "chars": "false", "force": "false", "direction": "\"-b\"", "min": "\"20\"", "anchoring": "\"\""}, "inputs": {"reference_sequence": {"id": "796d7152b6f678c7", "src": "hda", "uuid": "5c778596-6f7c-4484-a34c-c1d1f1d62b82"}, "query_sequence": {"id": "3352612fbd760959", "src": "hda", "uuid": "76bbb1a6-c800-4cf0-8e9e-71c76ff5ed94"}}, "outputs": {"output": {"id": "2cd83bd6d67a678e", "src": "hda", "uuid": "71196343-4536-4f57-ba54-12b66aeecaf3"}, "png_output": {"id": "3a48336881d2edb3", "src": "hda", "uuid": "4c7ccdc2-b6ec-40b6-bb8b-09c9edd0ff8c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "gnuplot 5.2 patchlevel 7\n", "tool_stderr": "Reading mummer file /galaxy/server/database/objects/7/1/1/dataset_71196343-4536-4f57-ba54-12b66aeecaf3.dat (use mummer -c)\nWriting plot files out.fplot, out.rplot, out.hplot\nWriting gnuplot script out.gp\nRendering plot out.png\nWARNING: Unable to run 'false out.gp', Inappropriate ioctl for device\n", "job_stdout": null, "job_stderr": null, "stdout": "gnuplot 5.2 patchlevel 7\n", "stderr": "Reading mummer file /galaxy/server/database/objects/7/1/1/dataset_71196343-4536-4f57-ba54-12b66aeecaf3.dat (use mummer -c)\nWriting plot files out.fplot, out.rplot, out.hplot\nWriting gnuplot script out.gp\nRendering plot out.png\nWARNING: Unable to run 'false out.gp', Inappropriate ioctl for device\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, exit_code: None, stderr: Reading mummer file /galaxy/server/database/objects/7/1/1/dataset_71196343-4536-4f57-ba54-12b66aeecaf3.dat (use mummer -c)\nWriting plot files out.fplot, out.rplot, out.hplot\nWriting gnuplot script out.gp\nRendering plot out.png\nWARNING: Unable to run 'false out.gp', Inappropriate ioctl for device\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, exit_code: None, stderr: Reading mummer file /galaxy/server/database/objects/7/1/1/dataset_71196343-4536-4f57-ba54-12b66aeecaf3.dat (use mummer -c)\nWriting plot files out.fplot, out.rplot, out.hplot\nWriting gnuplot script out.gp\nRendering plot out.png\nWARNING: Unable to run 'false out.gp', Inappropriate ioctl for device\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1, exit_code: None, stderr: Reading mummer file /galaxy/server/database/objects/7/1/1/dataset_71196343-4536-4f57-ba54-12b66aeecaf3.dat (use mummer -c)\nWriting plot files out.fplot, out.rplot, out.hplot\nWriting gnuplot script out.gp\nRendering plot out.png\nWARNING: Unable to run 'false out.gp', Inappropriate ioctl for device\n."], "status": "failure"}}, {"id": "music_construct_eset/0.1.1+galaxy0-0", "has_data": true, "data": {"tool_id": "music_construct_eset", "tool_version": "0.1.1+galaxy0", "test_index": 0, "time_seconds": 54.30440425872803, "inputs": {"exprs_file": {"src": "hda", "id": "09976a7dbbbe05e4"}, "pdata_file": {"src": "hda", "id": "56f34d6fb72980c7"}, "annotation": "hgu95av2", "metadata_0|row_names": "gender", "metadata_0|label_desc": "Patient gender", "metadata_1|row_names": "type", "metadata_1|label_desc": "Case/control status", "metadata_2|row_names": "score", "metadata_2|label_desc": "Tumor Progress on XYZ scale", "expdata|name": "Pierre Fermat", "expdata|lab": "Francis Galton Lab", "expdata|contact": "pfermat@lab.not.exist", "expdata|title": "Smoking-Cancer Experiment", "expdata|abstract": "An example ExpressionSet", "expdata|url": "www.lab.not.exist", "expdata|other_0|field": "notes", "expdata|other_0|comment": "Created in Galaxy", "expdata|other_1|field": "general", "expdata|other_1|comment": "Some other comment"}, "job": {"model_class": "Job", "id": "4e653a7883c2522a", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:02:28.244336", "update_time": "2024-09-04T19:03:01.845638", "galaxy_version": "24.1", "external_id": "gxy-57mgp", "handler": null, "job_runner_name": null, "command_line": "Rscript --vanilla '/galaxy/server/database/jobs_directory/000/118/configs/tmp9_psbma6'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": 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"outputs": {"out_rds": {"id": "c6346922b0157d20", "src": "hda", "uuid": "b415a51d-2afe-45d4-829b-5760e09eff94"}, "out_tab": {"id": "996a241e7cda9c62", "src": "hda", "uuid": "25fef56e-fcda-4767-9179-dd4a3665c243"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:02:46", "plugin": "core", "name": "end_epoch", "raw_value": "1725476566.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:02:42", "plugin": "core", "name": "start_epoch", "raw_value": "1725476562.0000000"}, {"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_construct_eset/0.1.1+galaxy0-0", "has_data": true, "data": {"tool_id": "music_construct_eset", "tool_version": "0.1.1+galaxy0", "test_index": 0, "time_seconds": 37.38440942764282, "inputs": {"exprs_file": {"src": "hda", "id": "0a3d65af2197e1a0"}, "pdata_file": {"src": "hda", "id": "62ad4617c55ecda6"}, "annotation": "hgu95av2", "metadata_0|row_names": "gender", "metadata_0|label_desc": "Patient gender", "metadata_1|row_names": "type", "metadata_1|label_desc": "Case/control status", "metadata_2|row_names": "score", "metadata_2|label_desc": "Tumor Progress on XYZ scale", "expdata|name": "Pierre Fermat", "expdata|lab": "Francis Galton Lab", "expdata|contact": "pfermat@lab.not.exist", "expdata|title": "Smoking-Cancer Experiment", "expdata|abstract": "An example ExpressionSet", "expdata|url": "www.lab.not.exist", "expdata|other_0|field": "notes", "expdata|other_0|comment": "Created in Galaxy", "expdata|other_1|field": "general", "expdata|other_1|comment": "Some other comment"}, "job": {"model_class": "Job", "id": "5f9881ffbde5739b", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:03:24.171763", "update_time": "2024-09-04T19:03:40.414064", "galaxy_version": "24.1", "external_id": "gxy-kqc98", "handler": null, "job_runner_name": null, "command_line": "Rscript --vanilla '/galaxy/server/database/jobs_directory/000/121/configs/tmpi0q7d0pb'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "expdata": "{\"abstract\": \"An example ExpressionSet\", \"contact\": \"pfermat@lab.not.exist\", \"lab\": \"Francis Galton Lab\", \"name\": \"Pierre Fermat\", \"other\": [{\"__index__\": 0, 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38.528616189956665, "inputs": {"input_file": {"src": "hda", "id": "5e2055f6e3145e43"}, "format": "fasta"}, "job": {"model_class": "Job", "id": "630aba36b9eb5918", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T18:38:09.470762", "update_time": "2024-09-04T18:38:27.275038", "galaxy_version": "24.1", "external_id": "gxy-j55hm", "handler": null, "job_runner_name": null, "command_line": "porechop -i '/galaxy/server/database/objects/b/2/8/dataset_b28e7408-74d6-49fa-91ce-60f594e8a07b.dat' --format 'fasta' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fasta'", "user_email": 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58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/24/working/out.fasta\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/b/2/8/dataset_b28e7408-74d6-49fa-91ce-60f594e8a07b.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 Short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR tail 1 63.3 63.3\n PCR tail 2 67.7 70.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/24/working/out.fasta\n\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 18:38:14", "plugin": "core", "name": "start_epoch", "raw_value": "1725475094.0000000"}, {"title": "Job End Time", "value": "2024-09-04 18:38:15", "plugin": "core", "name": "end_epoch", "raw_value": "1725475095.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "porechop/0.2.3-1", "has_data": true, "data": {"tool_id": "porechop", "tool_version": "0.2.3", "test_index": 1, "time_seconds": 34.229607820510864, "inputs": {"input_file": {"src": "hda", "id": "5f3f79c7a79748c1"}, "format": "fastq"}, "job": {"model_class": "Job", "id": "30329d3a85219f0d", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T18:38:47.889117", "update_time": "2024-09-04T18:39:01.597533", "galaxy_version": "24.1", "external_id": "gxy-x6nml", "handler": null, "job_runner_name": null, "command_line": "porechop -i '/galaxy/server/database/objects/b/5/2/dataset_b52eb124-a482-4eb6-9dbe-c008461972dc.dat' --format 'fastq' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fastq'", "user_email": "tests@fake.org", "command_version": "0.2.3_seqan2.1.1", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", "format": "\"fastq\""}, "inputs": {"input_file": {"id": "5f3f79c7a79748c1", "src": "hda", "uuid": "b52eb124-a482-4eb6-9dbe-c008461972dc"}}, "outputs": {"outfile": {"id": "b3e4a695bb40c31a", "src": "hda", "uuid": "362e6b66-2f85-4b04-a835-b9f187201b36"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/b/5/2/dataset_b52eb124-a482-4eb6-9dbe-c008461972dc.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 Short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR tail 1 63.3 63.3\n PCR tail 2 67.7 70.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/26/working/out.fastq\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/b/5/2/dataset_b52eb124-a482-4eb6-9dbe-c008461972dc.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 Short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR tail 1 63.3 63.3\n PCR tail 2 67.7 70.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/26/working/out.fastq\n\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 18:38:49", "plugin": "core", "name": "start_epoch", "raw_value": "1725475129.0000000"}, {"title": "Job End Time", "value": "2024-09-04 18:38:50", "plugin": "core", "name": "end_epoch", "raw_value": "1725475130.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "porechop/0.2.3-2", "has_data": true, "data": {"tool_id": "porechop", "tool_version": "0.2.3", "test_index": 2, "time_seconds": 24.477715253829956, "inputs": {"input_file": {"src": "hda", "id": "f72f493266f70991"}, "format": "fasta.gz"}, "job": {"model_class": "Job", "id": "36fea06678d221ff", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3", "state": "error", "exit_code": null, "create_time": "2024-09-04T18:39:21.971793", "update_time": "2024-09-04T18:39:26.733369", "galaxy_version": "24.1", "external_id": "gxy-fdq4b", "handler": null, "job_runner_name": null, "command_line": "porechop -i '/galaxy/server/database/objects/8/d/5/dataset_8d57a286-02c8-46d6-8595-2feb13093603.dat' --format 'fasta.gz' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fasta.gz'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", "format": "\"fasta.gz\""}, "inputs": {"input_file": {"id": "f72f493266f70991", "src": "hda", "uuid": "8d57a286-02c8-46d6-8595-2feb13093603"}}, "outputs": {"outfile": {"id": "4a3502ad1b1cd043", "src": "hda", "uuid": "adbc05b4-6865-4d52-8822-940affbbab7e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/8/d/5/dataset_8d57a286-02c8-46d6-8595-2feb13093603.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 Short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR tail 1 63.3 63.3\n PCR tail 2 67.7 70.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\npigz not found - using gzip to compress\n\nSaved result to /galaxy/server/database/jobs_directory/000/28/working/out.fasta.gz\n\n", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/8/d/5/dataset_8d57a286-02c8-46d6-8595-2feb13093603.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 Short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR tail 1 63.3 63.3\n PCR tail 2 67.7 70.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\npigz not found - using gzip to compress\n\nSaved result to /galaxy/server/database/jobs_directory/000/28/working/out.fasta.gz\n\n", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "porechop/0.2.3-3", "has_data": true, "data": {"tool_id": "porechop", "tool_version": "0.2.3", "test_index": 3, "time_seconds": 32.54041886329651, "inputs": {"input_file": {"src": "hda", "id": "041a65779e107113"}, "format": "fastq.gz"}, "job": {"model_class": "Job", "id": "abadc5621f631059", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T18:39:46.552701", "update_time": "2024-09-04T18:39:58.962171", "galaxy_version": "24.1", "external_id": "gxy-8c9f6", "handler": null, "job_runner_name": null, "command_line": "porechop -i '/galaxy/server/database/objects/e/6/c/dataset_e6cdc044-009a-4bb9-96b1-7e2a3a7297f4.dat' --format 'fastq.gz' --barcode_threshold '75.0' --barcode_diff '5.0' --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '150' --min_trim_size '4' --extra_end_trim '2' --end_threshold '75.0' --middle_threshold '85.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1000' -o 'out.fastq.gz'", "user_email": "tests@fake.org", "command_version": "0.2.3_seqan2.1.1", "params": {"format": "\"fastq.gz\"", "barcode_binning_settings": "{\"barcode_diff\": \"5.0\", \"barcode_threshold\": \"75.0\", \"discard_unassigned\": false, \"require_two_barcodes\": false}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "end_adapter_settings": "{\"end_size\": \"150\", \"end_threshold\": \"75.0\", \"extra_end_trim\": \"2\", \"min_trim_size\": \"4\"}", "middle_adapter_settings": "{\"discard_middle\": false, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"85.0\", \"min_split_read_size\": \"1000\", \"no_split\": false}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"fasta\""}, "inputs": {"input_file": {"id": "041a65779e107113", "src": "hda", "uuid": "e6cdc044-009a-4bb9-96b1-7e2a3a7297f4"}}, "outputs": {"outfile": {"id": "a59791e237ed6edc", "src": "hda", "uuid": "f1aa1c7e-d280-440f-b0f7-c36a47350c4b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/e/6/c/dataset_e6cdc044-009a-4bb9-96b1-7e2a3a7297f4.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 Short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR tail 1 63.3 63.3\n PCR tail 2 67.7 70.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\npigz not found - using gzip to compress\n\nSaved result to /galaxy/server/database/jobs_directory/000/30/working/out.fastq.gz\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/e/6/c/dataset_e6cdc044-009a-4bb9-96b1-7e2a3a7297f4.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n SQK-MAP006 62.2 63.6\n SQK-MAP006 Short 60.7 60.0\n PCR adapters 1 66.7 73.9\n PCR tail 1 63.3 63.3\n PCR tail 2 67.7 70.0\n 1D^2 part 1 62.1 58.8\n 1D^2 part 2 79.4 68.8\n Barcode 1 (reverse) 59.4 66.7\n Barcode 2 (reverse) 66.7 63.0\n Barcode 3 (reverse) 69.2 72.0\n Barcode 4 (reverse) 66.7 63.3\n Barcode 5 (reverse) 62.5 66.7\n Barcode 6 (reverse) 73.1 62.5\n Barcode 7 (reverse) 65.4 65.5\n Barcode 8 (reverse) 69.2 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 62.5 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 64.0\n Barcode 1 (forward) 65.4 61.5\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 73.1 68.0\n Barcode 4 (forward) 73.1 64.3\n Barcode 5 (forward) 62.5 66.7\n Barcode 6 (forward) 65.5 65.6\n Barcode 7 (forward) 73.1 66.7\n Barcode 8 (forward) 62.1 60.7\n Barcode 9 (forward) 68.0 70.8\n Barcode 10 (forward) 69.2 66.7\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 64.3 66.7\n Barcode 13 (forward) 64.3 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 70.8 65.5\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 70.4\n Barcode 19 (forward) 65.5 64.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 61.5 66.7\n Barcode 24 (forward) 66.7 65.4\n Barcode 25 (forward) 64.0 65.5\n Barcode 26 (forward) 72.0 72.0\n Barcode 27 (forward) 77.8 60.7\n Barcode 28 (forward) 65.5 66.7\n Barcode 29 (forward) 62.5 66.7\n Barcode 30 (forward) 68.0 65.4\n Barcode 31 (forward) 62.5 69.2\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 62.5 70.4\n Barcode 34 (forward) 64.0 62.5\n Barcode 35 (forward) 65.5 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 64.0 69.2\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 63.3\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 65.4 60.7\n Barcode 47 (forward) 65.5 64.0\n Barcode 48 (forward) 71.4 62.1\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 63.0\n Barcode 51 (forward) 69.2 64.3\n Barcode 52 (forward) 66.7 64.0\n Barcode 53 (forward) 67.9 69.0\n Barcode 54 (forward) 69.2 64.0\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 66.7 72.0\n Barcode 57 (forward) 69.0 60.0\n Barcode 58 (forward) 70.4 72.0\n Barcode 59 (forward) 56.7 66.7\n Barcode 60 (forward) 66.7 66.7\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 60.7\n Barcode 64 (forward) 69.2 66.7\n Barcode 65 (forward) 61.5 69.0\n Barcode 66 (forward) 64.3 63.0\n Barcode 67 (forward) 66.7 67.9\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 69.2 75.0\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 64.0 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 64.0\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 70.4 70.8\n Barcode 77 (forward) 65.4 64.3\n Barcode 78 (forward) 67.7 63.0\n Barcode 79 (forward) 70.8 69.2\n Barcode 80 (forward) 71.4 72.0\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.7 66.7\n Barcode 83 (forward) 69.2 68.0\n Barcode 84 (forward) 70.8 67.9\n Barcode 85 (forward) 61.5 60.0\n Barcode 86 (forward) 64.3 65.4\n Barcode 87 (forward) 66.7 65.4\n Barcode 88 (forward) 63.3 60.7\n Barcode 89 (forward) 69.2 66.7\n Barcode 90 (forward) 66.7 64.0\n Barcode 91 (forward) 68.0 64.3\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 69.2 73.1\n Barcode 94 (forward) 63.0 68.0\n Barcode 95 (forward) 64.0 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (74 bp removed)\n3 / 9 reads had adapters trimmed from their end (49 bp removed)\n\n\n\u001b[1m\u001b[4mSplitting reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were split based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\npigz not found - using gzip to compress\n\nSaved result to /galaxy/server/database/jobs_directory/000/30/working/out.fastq.gz\n\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "42949", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "42949.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 18:39:47", "plugin": "core", "name": "start_epoch", "raw_value": "1725475187.0000000"}, {"title": "Job End Time", "value": "2024-09-04 18:39:48", "plugin": "core", "name": "end_epoch", "raw_value": "1725475188.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "porechop/0.2.3-4", "has_data": true, "data": {"tool_id": "porechop", "tool_version": "0.2.3", "test_index": 4, "time_seconds": 32.914403676986694, "inputs": {"input_file": {"src": "hda", "id": "7e7265f765b33c01"}, "format": "fasta", "barcode_binning_settings|barcode_threshold": "70", "barcode_binning_settings|barcode_diff": "4", "barcode_binning_settings|require_two_barcodes": true, "barcode_binning_settings|discard_unassigned": true, "end_adapter_settings|end_size": "100", "end_adapter_settings|min_trim_size": "2", "end_adapter_settings|extra_end_trim": "1", "end_adapter_settings|end_threshold": "80", "middle_adapter_settings|discard_middle": true, "middle_adapter_settings|middle_threshold": "90", "middle_adapter_settings|min_split_read_size": "1500"}, "job": {"model_class": "Job", "id": "fd91d043720b0fcf", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T18:40:19.743756", "update_time": "2024-09-04T18:40:32.308533", "galaxy_version": "24.1", "external_id": "gxy-m2scj", "handler": null, "job_runner_name": null, "command_line": "porechop -i '/galaxy/server/database/objects/b/2/8/dataset_b2889160-a006-4bea-9adf-d9fe06801339.dat' --format 'fasta' --barcode_threshold '70.0' --barcode_diff '4.0' --require_two_barcodes --discard_unassigned --adapter_threshold '90.0' --check_reads '10000' --scoring_scheme '3,-6,-5,-2' --end_size '100' --min_trim_size '2' --extra_end_trim '1' --end_threshold '80.0' --discard_middle --middle_threshold '90.0' --extra_middle_trim_good_side '10' --extra_middle_trim_bad_side '100' --min_split_read_size '1500' -o 'out.fasta'", "user_email": "tests@fake.org", "command_version": "0.2.3_seqan2.1.1", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "middle_adapter_settings": "{\"discard_middle\": true, \"extra_middle_trim_bad_side\": \"100\", \"extra_middle_trim_good_side\": \"10\", \"middle_threshold\": \"90.0\", \"min_split_read_size\": \"1500\", \"no_split\": false}", "end_adapter_settings": "{\"end_size\": \"100\", \"end_threshold\": \"80.0\", \"extra_end_trim\": \"1\", \"min_trim_size\": \"2\"}", "adapter_search_settings": "{\"adapter_threshold\": \"90.0\", \"check_reads\": \"10000\", \"scoring_scheme\": \"3,-6,-5,-2\"}", "barcode_binning_settings": "{\"barcode_diff\": \"4.0\", \"barcode_threshold\": \"70.0\", \"discard_unassigned\": true, \"require_two_barcodes\": true}", "format": "\"fasta\""}, "inputs": {"input_file": {"id": "7e7265f765b33c01", "src": "hda", "uuid": "b2889160-a006-4bea-9adf-d9fe06801339"}}, "outputs": {"outfile": {"id": "771fbd7e1c575084", "src": "hda", "uuid": "a2536520-9eec-4b00-8744-99cc371730c2"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/b/2/8/dataset_b2889160-a006-4bea-9adf-d9fe06801339.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n SQK-MAP006 58.8 63.6\n SQK-MAP006 Short 58.6 57.7\n PCR adapters 1 66.7 73.9\n PCR tail 1 63.3 63.3\n PCR tail 2 67.7 70.0\n 1D^2 part 1 66.7 58.6\n 1D^2 part 2 79.4 68.8\n Barcode 1 (reverse) 58.3 66.7\n Barcode 2 (reverse) 66.7 50.0\n Barcode 3 (reverse) 69.2 69.2\n Barcode 4 (reverse) 66.7 61.5\n Barcode 5 (reverse) 62.5 69.2\n Barcode 6 (reverse) 65.4 62.5\n Barcode 7 (reverse) 62.5 65.5\n Barcode 8 (reverse) 59.3 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 57.7 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 55.2\n Barcode 1 (forward) 65.4 62.1\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 65.4 68.0\n Barcode 4 (forward) 63.3 64.3\n Barcode 5 (forward) 57.1 56.0\n Barcode 6 (forward) 45.7 63.0\n Barcode 7 (forward) 73.1 62.1\n Barcode 8 (forward) 62.1 60.6\n Barcode 9 (forward) 64.3 66.7\n Barcode 10 (forward) 61.8 68.0\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 60.6 66.7\n Barcode 13 (forward) 64.5 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 65.5 64.0\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 64.0\n Barcode 19 (forward) 64.5 63.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 57.9 65.5\n Barcode 24 (forward) 66.7 61.3\n Barcode 25 (forward) 59.4 68.0\n Barcode 26 (forward) 64.3 72.0\n Barcode 27 (forward) 61.3 59.4\n Barcode 28 (forward) 65.4 62.5\n Barcode 29 (forward) 57.7 62.5\n Barcode 30 (forward) 68.0 64.0\n Barcode 31 (forward) 62.1 61.5\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 46.2 70.4\n Barcode 34 (forward) 64.0 18.5\n Barcode 35 (forward) 64.3 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 61.5 62.5\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 62.5\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 66.7 60.7\n Barcode 47 (forward) 64.3 61.5\n Barcode 48 (forward) 71.4 65.4\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 57.1\n Barcode 51 (forward) 69.2 59.3\n Barcode 52 (forward) 62.5 64.0\n Barcode 53 (forward) 65.4 69.0\n Barcode 54 (forward) 69.2 62.1\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 62.5 64.0\n Barcode 57 (forward) 66.7 55.6\n Barcode 58 (forward) 67.7 66.7\n Barcode 59 (forward) 56.7 59.4\n Barcode 60 (forward) 66.7 63.0\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 62.5\n Barcode 64 (forward) 60.7 67.9\n Barcode 65 (forward) 61.5 62.5\n Barcode 66 (forward) 61.5 61.3\n Barcode 67 (forward) 66.7 60.0\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 65.5 66.7\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 60.7 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 63.6\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 60.6 64.0\n Barcode 77 (forward) 65.4 62.1\n Barcode 78 (forward) 66.7 63.3\n Barcode 79 (forward) 70.8 66.7\n Barcode 80 (forward) 62.5 66.7\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.0 66.7\n Barcode 83 (forward) 64.0 68.0\n Barcode 84 (forward) 64.5 67.9\n Barcode 85 (forward) 61.5 58.3\n Barcode 86 (forward) 64.3 66.7\n Barcode 87 (forward) 66.7 65.5\n Barcode 88 (forward) 63.3 61.5\n Barcode 89 (forward) 69.0 66.7\n Barcode 90 (forward) 64.3 61.3\n Barcode 91 (forward) 53.3 64.0\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 63.3 71.4\n Barcode 94 (forward) 61.5 64.5\n Barcode 95 (forward) 62.1 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (70 bp removed)\n3 / 9 reads had adapters trimmed from their end (46 bp removed)\n\n\n\u001b[1m\u001b[4mDiscarding reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were discarded based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/32/working/out.fasta\n\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "\n\u001b[1m\u001b[4mLoading reads\u001b[0m\n/galaxy/server/database/objects/b/2/8/dataset_b2889160-a006-4bea-9adf-d9fe06801339.dat\n9 reads loaded\n\n\n\u001b[1m\u001b[4mLooking for known adapter sets\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n Best \u001b[0m\n read Best \u001b[0m\n start read end\u001b[0m\n \u001b[4mSet %ID %ID \u001b[0m\n \u001b[32mSQK-NSK007 96.4 95.5\u001b[0m\n Rapid 62.5 0.0\n SQK-MAP006 58.8 63.6\n SQK-MAP006 Short 58.6 57.7\n PCR adapters 1 66.7 73.9\n PCR tail 1 63.3 63.3\n PCR tail 2 67.7 70.0\n 1D^2 part 1 66.7 58.6\n 1D^2 part 2 79.4 68.8\n Barcode 1 (reverse) 58.3 66.7\n Barcode 2 (reverse) 66.7 50.0\n Barcode 3 (reverse) 69.2 69.2\n Barcode 4 (reverse) 66.7 61.5\n Barcode 5 (reverse) 62.5 69.2\n Barcode 6 (reverse) 65.4 62.5\n Barcode 7 (reverse) 62.5 65.5\n Barcode 8 (reverse) 59.3 58.3\n Barcode 9 (reverse) 75.0 66.7\n Barcode 10 (reverse) 57.7 60.0\n Barcode 11 (reverse) 69.2 60.5\n Barcode 12 (reverse) 65.6 55.2\n Barcode 1 (forward) 65.4 62.1\n Barcode 2 (forward) 69.2 70.4\n Barcode 3 (forward) 65.4 68.0\n Barcode 4 (forward) 63.3 64.3\n Barcode 5 (forward) 57.1 56.0\n Barcode 6 (forward) 45.7 63.0\n Barcode 7 (forward) 73.1 62.1\n Barcode 8 (forward) 62.1 60.6\n Barcode 9 (forward) 64.3 66.7\n Barcode 10 (forward) 61.8 68.0\n Barcode 11 (forward) 65.4 60.7\n Barcode 12 (forward) 60.6 66.7\n Barcode 13 (forward) 64.5 69.2\n Barcode 14 (forward) 63.3 66.7\n Barcode 15 (forward) 66.7 66.7\n Barcode 16 (forward) 65.5 64.0\n Barcode 17 (forward) 69.2 66.7\n Barcode 18 (forward) 70.4 64.0\n Barcode 19 (forward) 64.5 63.0\n Barcode 20 (forward) 65.5 64.0\n Barcode 21 (forward) 64.3 66.7\n Barcode 22 (forward) 69.2 68.0\n Barcode 23 (forward) 57.9 65.5\n Barcode 24 (forward) 66.7 61.3\n Barcode 25 (forward) 59.4 68.0\n Barcode 26 (forward) 64.3 72.0\n Barcode 27 (forward) 61.3 59.4\n Barcode 28 (forward) 65.4 62.5\n Barcode 29 (forward) 57.7 62.5\n Barcode 30 (forward) 68.0 64.0\n Barcode 31 (forward) 62.1 61.5\n Barcode 32 (forward) 68.0 70.8\n Barcode 33 (forward) 46.2 70.4\n Barcode 34 (forward) 64.0 18.5\n Barcode 35 (forward) 64.3 65.4\n Barcode 36 (forward) 63.0 63.0\n Barcode 37 (forward) 67.9 64.3\n Barcode 38 (forward) 64.0 62.1\n Barcode 39 (forward) 61.5 62.5\n Barcode 40 (forward) 62.5 64.0\n Barcode 41 (forward) 68.0 65.5\n Barcode 42 (forward) 70.4 69.2\n Barcode 43 (forward) 63.3 62.5\n Barcode 44 (forward) 60.0 66.7\n Barcode 45 (forward) 73.1 65.4\n Barcode 46 (forward) 66.7 60.7\n Barcode 47 (forward) 64.3 61.5\n Barcode 48 (forward) 71.4 65.4\n Barcode 49 (forward) 69.2 62.1\n Barcode 50 (forward) 66.7 57.1\n Barcode 51 (forward) 69.2 59.3\n Barcode 52 (forward) 62.5 64.0\n Barcode 53 (forward) 65.4 69.0\n Barcode 54 (forward) 69.2 62.1\n Barcode 55 (forward) 66.7 73.1\n Barcode 56 (forward) 62.5 64.0\n Barcode 57 (forward) 66.7 55.6\n Barcode 58 (forward) 67.7 66.7\n Barcode 59 (forward) 56.7 59.4\n Barcode 60 (forward) 66.7 63.0\n Barcode 61 (forward) 70.8 65.5\n Barcode 62 (forward) 66.7 68.0\n Barcode 63 (forward) 66.7 62.5\n Barcode 64 (forward) 60.7 67.9\n Barcode 65 (forward) 61.5 62.5\n Barcode 66 (forward) 61.5 61.3\n Barcode 67 (forward) 66.7 60.0\n Barcode 68 (forward) 67.9 69.2\n Barcode 69 (forward) 65.5 66.7\n Barcode 70 (forward) 64.3 73.1\n Barcode 71 (forward) 60.7 71.4\n Barcode 72 (forward) 66.7 62.1\n Barcode 73 (forward) 67.7 63.6\n Barcode 74 (forward) 64.5 68.0\n Barcode 75 (forward) 65.4 65.5\n Barcode 76 (forward) 60.6 64.0\n Barcode 77 (forward) 65.4 62.1\n Barcode 78 (forward) 66.7 63.3\n Barcode 79 (forward) 70.8 66.7\n Barcode 80 (forward) 62.5 66.7\n Barcode 81 (forward) 68.0 66.7\n Barcode 82 (forward) 64.0 66.7\n Barcode 83 (forward) 64.0 68.0\n Barcode 84 (forward) 64.5 67.9\n Barcode 85 (forward) 61.5 58.3\n Barcode 86 (forward) 64.3 66.7\n Barcode 87 (forward) 66.7 65.5\n Barcode 88 (forward) 63.3 61.5\n Barcode 89 (forward) 69.0 66.7\n Barcode 90 (forward) 64.3 61.3\n Barcode 91 (forward) 53.3 64.0\n Barcode 92 (forward) 65.5 68.0\n Barcode 93 (forward) 63.3 71.4\n Barcode 94 (forward) 61.5 64.5\n Barcode 95 (forward) 62.1 63.3\n Barcode 96 (forward) 69.0 68.0\n\n\n\u001b[1m\u001b[4mTrimming adapters from read ends\u001b[0m\n SQK-NSK007_Y_Top: \u001b[31mAATGTACTTCGTTCAGTTACGTATTGCT\u001b[0m\n SQK-NSK007_Y_Bottom: \u001b[31mGCAATACGTAACTGAACGAAGT\u001b[0m\n\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r9 / 9 (100.0%)\n\n4 / 9 reads had adapters trimmed from their start (70 bp removed)\n3 / 9 reads had adapters trimmed from their end (46 bp removed)\n\n\n\u001b[1m\u001b[4mDiscarding reads containing middle adapters\u001b[0m\n\r0 / 9 (0.0%)\r9 / 9 (100.0%)\r10 / 9 (111.1%)\r9 / 9 (100.0%)\n\n4 / 9 reads were discarded based on middle adapters\n\n\n\u001b[1m\u001b[4mSaving trimmed reads to file\u001b[0m\n\nSaved result to /galaxy/server/database/jobs_directory/000/32/working/out.fasta\n\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", 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{\"__current_case__\": 1, \"bootnr\": \"30\", \"cln\": \"10\", \"clustnr\": \"10\", \"def\": \"no\", \"fselect\": false, \"knn\": \"5\", \"rseed\": \"17000\", \"samp\": \"10\", \"sat\": false}}"}, "inputs": {"inputrds": {"id": "c362dbc4308e5eb9", "src": "hda", "uuid": "ee3c3d6f-62ed-43ba-87dd-f7e1d510008e"}}, "outputs": {"outpdf": {"id": "6b5e034ca1871913", "src": "hda", "uuid": "7b1dc44e-4786-42e6-9763-27af8c3cc631"}, "outrdat": {"id": "50ef1274a196997c", "src": "hda", "uuid": "998c6e68-19f2-420b-9972-a38d26b9b4d7"}, "outassignments": {"id": "a2ed52c98c2993f8", "src": "hda", "uuid": "97217f5d-e02e-4f81-a94b-8798ea3915a7"}, "outgenelist": {"id": "91ad96a2a528808c", "src": "hda", "uuid": "c95469d1-e205-4461-b967-33c3f1f98099"}, "outlog": {"id": "37a41ae535aabcfd", "src": "hda", "uuid": "dcb471d2-faba-4313-87b9-a72b40722982"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", 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"id": "2a9705488e55de54", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:00:03.585927", "update_time": "2024-09-04T19:00:22.559930", "galaxy_version": "24.1", "external_id": "gxy-tskz5", "handler": null, "job_runner_name": null, "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/75557c0908a9/sam2interval/sam2interval.py' --input_sam_file='/galaxy/server/database/objects/4/c/f/dataset_4cf13732-a402-4693-a698-575c464eb042.dat' -p > '/galaxy/server/database/objects/7/b/6/dataset_7b698286-fe95-4f1f-adb4-546eacf2978e.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "print_all": "\"-p\""}, "inputs": {"input1": {"id": "db09421f3f1b1abc", "src": "hda", "uuid": 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"1.0000000"}]}, "status": "success"}}, {"id": "sam2interval/1.0.2-1", "has_data": true, "data": {"tool_id": "sam2interval", "tool_version": "1.0.2", "test_index": 1, "time_seconds": 33.62148475646973, "inputs": {"input1": {"src": "hda", "id": "db35a4950115a8ea"}, "print_all": ""}, "job": {"model_class": "Job", "id": "b11fec55df379ab0", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:00:43.495104", "update_time": "2024-09-04T19:00:56.230402", "galaxy_version": "24.1", "external_id": "gxy-kgxpk", "handler": null, "job_runner_name": null, "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/75557c0908a9/sam2interval/sam2interval.py' --input_sam_file='/galaxy/server/database/objects/3/9/0/dataset_39060254-0e3a-4dcd-bc01-64fc3fb1ce2a.dat' > '/galaxy/server/database/objects/d/4/d/dataset_d4d9c9ce-f6d5-4c33-85d5-f2b604cea2a6.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "print_all": "\"\""}, "inputs": {"input1": {"id": "db35a4950115a8ea", "src": "hda", "uuid": "39060254-0e3a-4dcd-bc01-64fc3fb1ce2a"}}, "outputs": {"out_file1": {"id": "a65dd01535592a4a", "src": "hda", "uuid": "d4d9c9ce-f6d5-4c33-85d5-f2b604cea2a6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-04 19:00:45", "plugin": "core", "name": "end_epoch", "raw_value": "1725476445.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:00:45", "plugin": "core", "name": "start_epoch", "raw_value": "1725476445.0000000"}, {"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": "sam2interval/1.0.2-2", "has_data": true, "data": {"tool_id": "sam2interval", "tool_version": "1.0.2", "test_index": 2, "time_seconds": 33.20151138305664, "inputs": {"input1": {"src": "hda", "id": "7f033b59caa88f29"}, "print_all": ""}, "job": {"model_class": "Job", "id": "7c61d8a2c0b19bd0", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.2", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:01:17.122716", "update_time": "2024-09-04T19:01:29.744637", "galaxy_version": "24.1", "external_id": "gxy-vq98g", "handler": null, "job_runner_name": null, "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/75557c0908a9/sam2interval/sam2interval.py' --input_sam_file='/galaxy/server/database/objects/5/2/7/dataset_5278ba70-ebe2-4646-a48b-f0db5de3d448.dat' > '/galaxy/server/database/objects/1/0/d/dataset_10de7427-071e-493b-883e-47743fa3918b.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "print_all": "\"\""}, "inputs": {"input1": {"id": "7f033b59caa88f29", "src": "hda", "uuid": "5278ba70-ebe2-4646-a48b-f0db5de3d448"}}, "outputs": {"out_file1": {"id": "ca8200a9c07f5244", "src": "hda", "uuid": "10de7427-071e-493b-883e-47743fa3918b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-04 19:01:19", "plugin": "core", "name": "end_epoch", "raw_value": "1725476479.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:01:19", "plugin": "core", "name": "start_epoch", "raw_value": "1725476479.0000000"}, {"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_flagstat/2.0.3-0", "has_data": true, "data": {"tool_id": "samtools_flagstat", "tool_version": "2.0.3", "test_index": 0, "time_seconds": 34.92231106758118, "inputs": {"input1": {"src": "hda", "id": "2ad37a77b3e1842f"}}, "job": {"model_class": "Job", "id": "0ad7490c940f20ad", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:01:51.473568", "update_time": "2024-09-04T19:02:06.070591", "galaxy_version": "24.1", "external_id": "gxy-9jhzw", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools flagstat -@ $addthreads '/galaxy/server/database/objects/3/3/1/dataset_3310a7a5-e9d1-4d22-ba84-a1f85e3def19.dat' > '/galaxy/server/database/objects/a/9/e/dataset_a9e44153-ecf0-4d57-944a-b49f3f099494.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input1": {"id": "2ad37a77b3e1842f", "src": "hda", "uuid": "3310a7a5-e9d1-4d22-ba84-a1f85e3def19"}}, "outputs": {"output1": {"id": "d5dacb7eaf50df39", "src": "hda", "uuid": "a9e44153-ecf0-4d57-944a-b49f3f099494"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-04 19:01:55", "plugin": "core", "name": "end_epoch", "raw_value": "1725476515.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:01:55", "plugin": "core", "name": "start_epoch", "raw_value": "1725476515.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.7.1+galaxy0-0", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.7.1+galaxy0", "test_index": 0, "time_seconds": 57.19379019737244, "inputs": {"adata": {"src": "hda", "id": "3629d3de3493ef83"}, "method|filter|min_counts": "3", "method|filter|filter": "min_counts", "method|method": "pp.filter_cells", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "c4029a77e6fda276", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:13:04.187183", "update_time": "2024-09-04T19:13:40.348497", "galaxy_version": "24.1", "external_id": "gxy-wzwc6", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/9/2/0/dataset_92067362-c54a-4979-9e0f-b76f1d1f779a.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/135/configs/tmpjwsyzfxt' > '/galaxy/server/database/objects/b/b/b/dataset_bbbe2401-52bb-4158-ac0f-47a2ae971ffb.dat' && python '/galaxy/server/database/jobs_directory/000/135/configs/tmpjwsyzfxt' >> '/galaxy/server/database/objects/b/b/b/dataset_bbbe2401-52bb-4158-ac0f-47a2ae971ffb.dat' && ls . >> '/galaxy/server/database/objects/b/b/b/dataset_bbbe2401-52bb-4158-ac0f-47a2ae971ffb.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 0, \"filter\": {\"__current_case__\": 0, \"filter\": \"min_counts\", \"min_counts\": \"3\"}, \"method\": \"pp.filter_cells\"}"}, "inputs": {"adata": {"id": "3629d3de3493ef83", "src": "hda", "uuid": "92067362-c54a-4979-9e0f-b76f1d1f779a"}}, "outputs": {"anndata_out": {"id": "e7f9c71e17919e17", "src": "hda", "uuid": "fa5f9eb6-52f9-4853-b004-6dbda14bca3c"}, "hidden_output": {"id": "d7721f302d42d05e", "src": "hda", "uuid": "bbbe2401-52bb-4158-ac0f-47a2ae971ffb"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 336 \u00d7 11\n[obs]\n- cell_type\n- n_counts\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 336 \u00d7 11\n[obs]\n- cell_type\n- n_counts\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:13:24", "plugin": "core", "name": "end_epoch", "raw_value": "1725477204.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:13:21", "plugin": "core", "name": "start_epoch", "raw_value": "1725477201.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.7.1+galaxy0-1", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.7.1+galaxy0", "test_index": 1, "time_seconds": 29.141318559646606, "inputs": {"adata": {"src": "hda", "id": "da8dabdc7a6c9084"}, "method|filter|max_genes": "100", "method|filter|filter": "max_genes", "method|method": "pp.filter_cells", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "0a3ea1b885987c08", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0", "state": "error", "exit_code": null, "create_time": "2024-09-04T19:14:01.874664", "update_time": "2024-09-04T19:14:10.613857", "galaxy_version": "24.1", "external_id": "gxy-cm9w5", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/3/1/5/dataset_31560881-ef28-4f42-9279-93241afca87a.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/137/configs/tmpu5om38ov' > '/galaxy/server/database/objects/9/8/7/dataset_9871714f-f2ce-4a0f-bd7c-dba53bbd7541.dat' && python '/galaxy/server/database/jobs_directory/000/137/configs/tmpu5om38ov' >> '/galaxy/server/database/objects/9/8/7/dataset_9871714f-f2ce-4a0f-bd7c-dba53bbd7541.dat' && ls . >> '/galaxy/server/database/objects/9/8/7/dataset_9871714f-f2ce-4a0f-bd7c-dba53bbd7541.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 0, \"filter\": {\"__current_case__\": 3, \"filter\": \"max_genes\", \"max_genes\": \"100\"}, \"method\": \"pp.filter_cells\"}"}, "inputs": {"adata": {"id": "da8dabdc7a6c9084", "src": "hda", "uuid": "31560881-ef28-4f42-9279-93241afca87a"}}, "outputs": {"anndata_out": {"id": "bec25e6b1a0850d8", "src": "hda", "uuid": "850fcd68-6380-4967-b7ab-508770596108"}, "hidden_output": {"id": "ae6bb488985fa333", "src": "hda", "uuid": "9871714f-f2ce-4a0f-bd7c-dba53bbd7541"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n- n_genes\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": null, "job_stderr": null, "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n- n_genes\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n."], "status": "failure"}}, {"id": "scanpy_filter/1.7.1+galaxy0-2", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.7.1+galaxy0", "test_index": 2, "time_seconds": 37.67886018753052, "inputs": {"adata": {"src": "hda", "id": "bd8a2d47f0bfc8fe"}, "method|filter|min_counts": "3", "method|filter|filter": "min_counts", "method|method": "pp.filter_genes", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "f777042bd482ff7f", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:14:31.619790", "update_time": "2024-09-04T19:14:47.459366", "galaxy_version": "24.1", "external_id": "gxy-nsbj2", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/c/3/d/dataset_c3d7b824-2b3c-49af-a667-10ac6e3c0957.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/139/configs/tmpbuj85pa2' > '/galaxy/server/database/objects/5/6/1/dataset_5616a376-f51a-4e5c-a69e-e3a1ac13d1da.dat' && python '/galaxy/server/database/jobs_directory/000/139/configs/tmpbuj85pa2' >> '/galaxy/server/database/objects/5/6/1/dataset_5616a376-f51a-4e5c-a69e-e3a1ac13d1da.dat' && ls . >> '/galaxy/server/database/objects/5/6/1/dataset_5616a376-f51a-4e5c-a69e-e3a1ac13d1da.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 1, \"filter\": {\"__current_case__\": 0, \"filter\": \"min_counts\", \"min_counts\": \"3\"}, \"method\": \"pp.filter_genes\"}"}, "inputs": {"adata": {"id": "bd8a2d47f0bfc8fe", "src": "hda", "uuid": "c3d7b824-2b3c-49af-a667-10ac6e3c0957"}}, "outputs": {"anndata_out": {"id": "7b9f04f85ff9a346", "src": "hda", "uuid": "e16a3f99-f215-40a5-ae75-b8c3bccf7da0"}, "hidden_output": {"id": "de86d93837b1c051", "src": "hda", "uuid": "5616a376-f51a-4e5c-a69e-e3a1ac13d1da"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[var]\n- n_counts\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- cell_type\n[var]\n- n_counts\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:14:36", "plugin": "core", "name": "end_epoch", "raw_value": "1725477276.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:14:33", "plugin": "core", "name": "start_epoch", "raw_value": "1725477273.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.7.1+galaxy0-3", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.7.1+galaxy0", "test_index": 3, "time_seconds": 37.94441342353821, "inputs": {"adata": {"src": "hda", "id": "420d825b134dd8ae"}, "method|flavor|min_mean": "0.0125", "method|flavor|max_mean": "3", "method|flavor|min_disp": "0.5", "method|flavor|flavor": "seurat", "method|n_bins": "20", "method|subset": false, "method|method": "pp.highly_variable_genes", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "6486d0127152cd1a", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:15:09.863499", "update_time": "2024-09-04T19:15:25.765048", "galaxy_version": "24.1", "external_id": "gxy-z5rkh", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/d/3/2/dataset_d327fb75-1f57-46fe-b529-723560b2480e.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/141/configs/tmpo_lxeszi' > '/galaxy/server/database/objects/7/b/c/dataset_7bc7b37b-2cbe-4cc7-ba86-2a8bb98a8e02.dat' && python '/galaxy/server/database/jobs_directory/000/141/configs/tmpo_lxeszi' >> '/galaxy/server/database/objects/7/b/c/dataset_7bc7b37b-2cbe-4cc7-ba86-2a8bb98a8e02.dat' && ls . >> '/galaxy/server/database/objects/7/b/c/dataset_7bc7b37b-2cbe-4cc7-ba86-2a8bb98a8e02.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 3, \"flavor\": {\"__current_case__\": 0, \"flavor\": \"seurat\", \"max_disp\": \"\", \"max_mean\": \"3.0\", \"min_disp\": \"0.5\", \"min_mean\": \"0.0125\"}, \"method\": \"pp.highly_variable_genes\", \"n_bins\": \"20\", \"subset\": false}"}, "inputs": {"adata": {"id": "420d825b134dd8ae", "src": "hda", "uuid": "d327fb75-1f57-46fe-b529-723560b2480e"}}, "outputs": {"anndata_out": {"id": "dcb59ca1e2bedae5", "src": "hda", "uuid": "a7928732-f363-4608-a460-93df733c3417"}, "hidden_output": {"id": "628c8d60950464cb", "src": "hda", "uuid": "7bc7b37b-2cbe-4cc7-ba86-2a8bb98a8e02"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- blobs\n[var]\n- highly_variable\n- means\n- dispersions\n- dispersions_norm\n[uns]\n- hvg\n", "tool_stderr": "... storing 'blobs' as categorical\n", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 640 \u00d7 11\n[obs]\n- blobs\n[var]\n- highly_variable\n- means\n- dispersions\n- dispersions_norm\n[uns]\n- hvg\n", "stderr": "... storing 'blobs' as categorical\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:15:14", "plugin": "core", "name": "end_epoch", "raw_value": "1725477314.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:15:11", "plugin": "core", "name": "start_epoch", "raw_value": "1725477311.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.7.1+galaxy0-4", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.7.1+galaxy0", "test_index": 4, "time_seconds": 11.126343488693237, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "scanpy_filter/1.7.1+galaxy0-5", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.7.1+galaxy0", "test_index": 5, "time_seconds": 36.1782488822937, "inputs": {"adata": {"src": "hda", "id": "4ac27096f6aeda9a"}, "method|type|fraction": "0.5", "method|type|type": "fraction", "method|random_state": "0", "method|method": "pp.subsample", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "2652ae4d24003cae", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:15:58.343278", "update_time": "2024-09-04T19:16:13.467537", "galaxy_version": "24.1", "external_id": "gxy-jmdxl", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/3/4/2/dataset_342a8840-3afe-45ef-886e-7db3cc9ab5bb.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/144/configs/tmp9aghycul' > '/galaxy/server/database/objects/8/a/6/dataset_8a62b8f6-95d0-4b69-bf01-cfefcccc965a.dat' && python '/galaxy/server/database/jobs_directory/000/144/configs/tmp9aghycul' >> '/galaxy/server/database/objects/8/a/6/dataset_8a62b8f6-95d0-4b69-bf01-cfefcccc965a.dat' && ls . >> '/galaxy/server/database/objects/8/a/6/dataset_8a62b8f6-95d0-4b69-bf01-cfefcccc965a.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 4, \"method\": \"pp.subsample\", \"random_state\": \"0\", \"type\": {\"__current_case__\": 0, \"fraction\": \"0.5\", \"type\": \"fraction\"}}"}, "inputs": {"adata": {"id": "4ac27096f6aeda9a", "src": "hda", "uuid": "342a8840-3afe-45ef-886e-7db3cc9ab5bb"}}, "outputs": {"anndata_out": {"id": "3e58ec7616f1205f", "src": "hda", "uuid": "f94270cb-b89d-45de-90f8-db1802af8ce7"}, "hidden_output": {"id": "f4685a529851a943", "src": "hda", "uuid": "8a62b8f6-95d0-4b69-bf01-cfefcccc965a"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 320 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 320 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\nObservation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:16:03", "plugin": "core", "name": "end_epoch", "raw_value": "1725477363.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:16:00", "plugin": "core", "name": "start_epoch", "raw_value": "1725477360.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.7.1+galaxy0-6", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.7.1+galaxy0", "test_index": 6, "time_seconds": 35.98186469078064, "inputs": {"adata": {"src": "hda", "id": "8581531e8af40469"}, "method|type|n_obs": "10", "method|type|type": "n_obs", "method|random_state": "0", "method|method": "pp.subsample", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "dce29b8e275e623e", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:16:34.620415", "update_time": "2024-09-04T19:16:49.610109", "galaxy_version": "24.1", "external_id": "gxy-f4bzt", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/b/d/9/dataset_bd9960c3-7690-4cb7-ac04-9fd0d2763800.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/146/configs/tmp7sbr4v4v' > '/galaxy/server/database/objects/0/c/c/dataset_0cc1709c-bddb-4327-8d2f-4ee4491bc75f.dat' && python '/galaxy/server/database/jobs_directory/000/146/configs/tmp7sbr4v4v' >> '/galaxy/server/database/objects/0/c/c/dataset_0cc1709c-bddb-4327-8d2f-4ee4491bc75f.dat' && ls . >> '/galaxy/server/database/objects/0/c/c/dataset_0cc1709c-bddb-4327-8d2f-4ee4491bc75f.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 4, \"method\": \"pp.subsample\", \"random_state\": \"0\", \"type\": {\"__current_case__\": 1, \"n_obs\": \"10\", \"type\": \"n_obs\"}}"}, "inputs": {"adata": {"id": "8581531e8af40469", "src": "hda", "uuid": "bd9960c3-7690-4cb7-ac04-9fd0d2763800"}}, "outputs": {"anndata_out": {"id": "ab9283a21447f61d", "src": "hda", "uuid": "7d50d92a-5877-48fb-97d4-7772c7c651a2"}, "hidden_output": {"id": "a6ed15d552ab324f", "src": "hda", "uuid": "0cc1709c-bddb-4327-8d2f-4ee4491bc75f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 10 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 10 \u00d7 11\n[obs]\n- cell_type\n[uns]\n- cell_type_colors\n- highlights\n- iroot\n", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:16:39", "plugin": "core", "name": "end_epoch", "raw_value": "1725477399.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:16:35", "plugin": "core", "name": "start_epoch", "raw_value": "1725477395.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_filter/1.7.1+galaxy0-7", "has_data": true, "data": {"tool_id": "scanpy_filter", "tool_version": "1.7.1+galaxy0", "test_index": 7, "time_seconds": 65.05054879188538, "inputs": {"adata": {"src": "hda", "id": "50b51c1a8259ae45"}, "method|total_counts": "20000", "method|random_state": "0", "method|replace": false, "method|method": "pp.downsample_counts", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "44febf85122db16d", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:17:12.425794", "update_time": "2024-09-04T19:17:54.566414", "galaxy_version": "24.1", "external_id": "gxy-vz7gj", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/3/9/b/dataset_39b2000d-0770-4f1d-aa9c-b3b979b6723d.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/148/configs/tmpfvz5vouq' > '/galaxy/server/database/objects/4/a/0/dataset_4a03964d-da2f-4d9c-b767-38f11dcdbf86.dat' && python '/galaxy/server/database/jobs_directory/000/148/configs/tmpfvz5vouq' >> '/galaxy/server/database/objects/4/a/0/dataset_4a03964d-da2f-4d9c-b767-38f11dcdbf86.dat' && ls . >> '/galaxy/server/database/objects/4/a/0/dataset_4a03964d-da2f-4d9c-b767-38f11dcdbf86.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 5, \"counts_per_cell\": \"\", \"method\": \"pp.downsample_counts\", \"random_state\": \"0\", \"replace\": false, \"total_counts\": \"20000\"}"}, "inputs": {"adata": {"id": "50b51c1a8259ae45", "src": "hda", "uuid": "39b2000d-0770-4f1d-aa9c-b3b979b6723d"}}, "outputs": {"anndata_out": {"id": "ce2b212e4c7678b5", "src": "hda", "uuid": "5779864e-cea5-4030-ae8c-304a95fd2755"}, "hidden_output": {"id": "36bd71d0363208af", "src": "hda", "uuid": "4a03964d-da2f-4d9c-b767-38f11dcdbf86"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[n_obs \u00d7 n_vars]\n- 1000 \u00d7 1000\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[n_obs \u00d7 n_vars]\n- 1000 \u00d7 1000\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "30 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "30.0000000"}, {"title": "Job End Time", "value": "2024-09-04 19:17:44", "plugin": "core", "name": "end_epoch", "raw_value": "1725477464.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:17:14", "plugin": "core", "name": "start_epoch", "raw_value": "1725477434.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "scanpy_normalise_data/1.8.1+3+galaxy0-0", "has_data": true, "data": {"tool_id": "scanpy_normalise_data", "tool_version": "1.8.1+3+galaxy0", "test_index": 0, "time_seconds": 0.4562826156616211, "execution_problem": "Input staging problem: Test input file (filter_genes.h5) cannot be found.", "status": "error"}}, {"id": "scanpy_normalise_data/1.8.1+3+galaxy0-0", "has_data": true, "data": {"tool_id": "scanpy_normalise_data", "tool_version": "1.8.1+3+galaxy0", "test_index": 0, "time_seconds": 0.452517032623291, "execution_problem": "Input staging problem: Test input file (filter_genes.h5) cannot be found.", "status": "error"}}, {"id": "vcfgeno2haplo/1.0.0_rc3+galaxy0-0", "has_data": true, "data": {"tool_id": "vcfgeno2haplo", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 0, "time_seconds": 39.917813777923584, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "a3f2453dec6e5572"}, "reference_source|input_vcf": {"src": "hda", "id": "7570b7ee69bb7816"}, "reference_source|reference_source_selector": "history", "window_size": "5000", "output_option": true}, "job": {"model_class": "Job", "id": "a227886523b7fe16", "history_id": "3cbec5b19229f469", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-04T19:29:18.812399", "update_time": "2024-09-04T19:29:37.532829", "galaxy_version": "24.1", "external_id": "gxy-rpvrc", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/7/f/0/dataset_7f0c28ec-067b-426e-a57f-b78ac37bfa2a.dat' 'localref.fa' && vcfgeno2haplo -o -w 5000 -r \"localref.fa\" \"/galaxy/server/database/objects/f/d/a/dataset_fdaeaa59-8946-4432-a38e-e3575bcfea7f.dat\" > \"/galaxy/server/database/objects/0/2/6/dataset_026907d9-ff1d-4b2a-8556-104dbd6ee866.dat\"", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_option": "true", "window_size": "\"5000\"", "reference_source": "{\"__current_case__\": 1, \"input_vcf\": {\"values\": [{\"id\": 275, \"src\": \"hda\"}]}, \"ref_file\": {\"values\": [{\"id\": 274, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|ref_file": {"id": "a3f2453dec6e5572", "src": "hda", "uuid": "7f0c28ec-067b-426e-a57f-b78ac37bfa2a"}, "reference_source|input_vcf": {"id": "7570b7ee69bb7816", "src": "hda", "uuid": "fdaeaa59-8946-4432-a38e-e3575bcfea7f"}}, "outputs": {"out_file1": {"id": "2fd39996c67856c4", "src": "hda", "uuid": "026907d9-ff1d-4b2a-8556-104dbd6ee866"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "index file localref.fa.fai not found, generating...\nno alternate alleles remain at phiX174:1015 after haplotype validation\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "index file localref.fa.fai not found, generating...\nno alternate alleles remain at phiX174:1015 after haplotype validation\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-04 19:29:25", "plugin": "core", "name": "end_epoch", "raw_value": "1725478165.0000000"}, {"title": "Job Start Time", "value": "2024-09-04 19:29:25", "plugin": "core", "name": "start_epoch", "raw_value": "1725478165.0000000"}, {"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"}}], "galaxy_url": "http://35.229.67.235:8000/galaxy/"} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/results.xunit b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/results.xunit new file mode 100644 index 000000000..9daeba7d2 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-04-18-15-1/results.xunit @@ -0,0 +1,972 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + line 21.Use of uninitialized value within %Circos::Error::GROUPERROR in uc at /usr/local/bin/../lib/Circos/Error.pm line 354, line 21.Use of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781, line 21.Use of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.Use of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.Use of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781, line 1214.Use of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.Use of uninitialized value in subroutine entry at /usr/local/bin/../lib/Circos/Configuration.pm line 781.Use of uninitialized value within %Circos::Error::GROUPERROR in uc at /usr/local/bin/../lib/Circos/Error.pm line 354. + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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collection_operations + tool_panel_section_label: Collection Operations +- name: deeptools_multi_bam_summary + owner: bgruening + revisions: + - 78f405266706 + tool_panel_section_id: deeptools + tool_panel_section_label: deepTools +- name: fastq_paired_end_deinterlacer + owner: devteam + revisions: + - f3936d0632cb + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: circos + owner: iuc + revisions: + - df7356989ac1 + tool_panel_section_id: graph_display_data + tool_panel_section_label: Graph/Display Data +- name: mummer_mummer + owner: iuc + revisions: + - 48823c9635a4 + tool_panel_section_id: multiple_alignments + tool_panel_section_label: Multiple Alignments +- name: porechop + owner: iuc + revisions: + - 93d623d9979c + tool_panel_section_id: nanopore + tool_panel_section_label: Nanopore +- name: limma_voom + owner: iuc + revisions: + - 0921444c832d + - d6f5fa4ee473 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq +- name: sam2interval + owner: devteam + revisions: + - 75557c0908a9 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: samtools_flagstat + owner: devteam + revisions: + - 22970df7a40e + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: music_construct_eset + owner: bgruening + revisions: + - 282819d09a4f + - 2cfd0db49bbc + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: raceid_clustering + owner: iuc + revisions: + - a4b734cd253b + - f911a64454fb + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_filter + owner: iuc + revisions: + - b409c2486353 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_normalise_data + owner: ebi-gxa + revisions: + - 439f7f939d46 + - 463d4fa8f5ec + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: annotatemyids + owner: iuc + revisions: + - 44018dd6b447 + - fe3ca740a485 + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: diff + owner: bgruening + revisions: + - 156d0908e232 + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: bcftools_consensus + owner: iuc + revisions: + - d6dc477167f8 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: bcftools_plugin_impute_info + owner: iuc + revisions: + - 776ad0b21536 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: bcftools_query + owner: iuc + revisions: + - c9c5718edc19 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: vcfgeno2haplo + owner: devteam + revisions: + - a3dea556218d + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: ivar_trim + owner: iuc + revisions: + - db536ad45f28 + tool_panel_section_id: virology + tool_panel_section_label: Virology