From 580449c101cf4e474d8abc2e0aecf9deca6df762 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Sun, 1 Sep 2024 07:22:41 +0000 Subject: [PATCH] Updating anvil-edge README for edge-24-09-01-06-11-1 --- reports/anvil-edge/README.md | 2 +- reports/anvil-edge/tool-tests/chunks.json | 10 +- .../edge-24-09-01-06-11-1/chunk.json | 7 + .../edge-24-09-01-06-11-1/chunk.txt | 23 + .../errors/0819d429057bf8a0.json | 45 + .../errors/0fdb98639d6d499e.json | 45 + .../errors/15b628f3a8b45d2c.json | 45 + .../errors/17b9af32bdd92c3c.json | 45 + .../errors/1e422eebd2ee4ea3.json | 45 + .../errors/1ed84d616d66eb3e.json | 45 + .../errors/28e6fe619e9e1c2d.json | 56 ++ .../errors/2a40b2de8c94c1df.json | 45 + .../errors/2ebb3ad5094e871e.json | 45 + .../errors/2fe69f8fdae96ff9.json | 45 + .../errors/2ff7fac60df81cb9.json | 45 + .../errors/3efcd2344b65bd51.json | 45 + .../errors/452f1202fd627b61.json | 45 + .../errors/489a622667d2a7f4.json | 45 + .../errors/4b5dad8e931c522a.json | 45 + .../errors/5757eb3d49d1b901.json | 45 + .../errors/581ba2a7c02bc8c2.json | 51 ++ .../errors/653676bc098c5fdb.json | 45 + .../errors/88559008d97b3013.json | 81 ++ .../errors/9232ef9a71209bf9.json | 45 + .../errors/936d50d74e2f64ae.json | 55 ++ .../errors/96378b79f935ff5d.json | 45 + .../errors/a0b1a34be295a041.json | 45 + .../errors/a7f57026c8e757f7.json | 45 + .../errors/ba0c68d0fb174b9d.json | 45 + .../errors/cdb8918ea01b68fe.json | 45 + .../errors/d52dd58fbb5ccf5d.json | 56 ++ .../errors/d69fe4bde36ad371.json | 45 + .../errors/d88f6a5fa816379a.json | 45 + .../errors/d90f49ab235eaae5.json | 45 + .../errors/e73af671a892f31c.json | 45 + .../errors/fc7e18a9a612ec6a.json | 45 + .../edge-24-09-01-06-11-1/job-metrics.csv | 297 +++++++ .../tool-tests/edge-24-09-01-06-11-1/jobs.txt | 296 +++++++ .../edge-24-09-01-06-11-1/results.html | 291 +++++++ .../edge-24-09-01-06-11-1/results.json | 1 + .../edge-24-09-01-06-11-1/results.xunit | 776 ++++++++++++++++++ .../edge-24-09-01-06-11-1/tools.yml | 120 +++ 42 files changed, 3331 insertions(+), 6 deletions(-) create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/chunk.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/chunk.txt create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/0819d429057bf8a0.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/0fdb98639d6d499e.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/15b628f3a8b45d2c.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/17b9af32bdd92c3c.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/1e422eebd2ee4ea3.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/1ed84d616d66eb3e.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/28e6fe619e9e1c2d.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/2a40b2de8c94c1df.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/2ebb3ad5094e871e.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/2fe69f8fdae96ff9.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/2ff7fac60df81cb9.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/3efcd2344b65bd51.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/452f1202fd627b61.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/489a622667d2a7f4.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/4b5dad8e931c522a.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/5757eb3d49d1b901.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/581ba2a7c02bc8c2.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/653676bc098c5fdb.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/88559008d97b3013.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/9232ef9a71209bf9.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/936d50d74e2f64ae.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/96378b79f935ff5d.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/a0b1a34be295a041.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/a7f57026c8e757f7.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/ba0c68d0fb174b9d.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/cdb8918ea01b68fe.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/d52dd58fbb5ccf5d.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/d69fe4bde36ad371.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/d88f6a5fa816379a.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/d90f49ab235eaae5.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/e73af671a892f31c.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/fc7e18a9a612ec6a.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/job-metrics.csv create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/jobs.txt create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/results.html create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/results.json create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/results.xunit create mode 100644 reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/tools.yml diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md index 7a4c46ad4..f4c35fe0e 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 Aug 26 06:26:05 2024Mon Aug 19 06:25:37 2024
1ToolsetMon Aug 26 18:31:46 2024Mon Aug 19 18:31:01 2024
2ToolsetTue Aug 27 06:26:39 2024Tue Aug 20 06:25:04 2024
3ToolsetTue Aug 27 18:39:36 2024Tue Aug 20 18:31:06 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 Aug 25 06:24:42 2024Sun Aug 18 06:23:42 2024
13ToolsetSun Aug 25 18:29:56 2024Sun Aug 18 18:29:49 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Aug 26 06:26:05 2024Mon Aug 19 06:25:37 2024
1ToolsetMon Aug 26 18:31:46 2024Mon Aug 19 18:31:01 2024
2ToolsetTue Aug 27 06:26:39 2024Tue Aug 20 06:25:04 2024
3ToolsetTue Aug 27 18:39:36 2024Tue Aug 20 18:31:06 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 Aug 25 18:29:56 2024Sun Aug 18 18:29:49 2024
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json index 1d294c389..5fa8b9095 100644 --- a/reports/anvil-edge/tool-tests/chunks.json +++ b/reports/anvil-edge/tool-tests/chunks.json @@ -70,11 +70,11 @@ "date2": "Sat Aug 24 06:23:31 2024" }, "12": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-25-06-09-1/results.html", - "date1": "Sun Aug 25 06:24:42 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-25-06-09-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-18-06-09-1/results.html", - "date2": "Sun Aug 18 06:23:42 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/results.html", + "date1": "Sun Sep 01 06:26:20 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-25-06-09-1/results.html", + "date2": "Sun Aug 25 06:24:42 2024" }, "13": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-25-18-14-1/results.html", diff --git a/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/chunk.json new file mode 100644 index 000000000..fe235bdec --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/chunk.json @@ -0,0 +1,7 @@ +{ + "12": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/results.html", + "date1": "Sun Sep 01 06:26:20 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/chunk.txt new file mode 100644 index 000000000..179bf57d8 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/chunk.txt @@ -0,0 +1,23 @@ +-t deeptools_compute_matrix --tool-version 514fa53b5efb +-t deeptools_bam_coverage --tool-version bb1e4f63e0e6 +-t multiqc --tool-version 75c93c70d094 +-t multiqc --tool-version 9a913cdee30e +-t multiqc --tool-version df99138d2776 +-t lastz --tool-version e7f19d6a9af8 +-t nanoplot --tool-version edbb6c5028f5 +-t poretools_extract --tool-version 7e4f1ed70187 +-t pileup_interval --tool-version 9c1c0b947e46 +-t samtools_depth --tool-version 44de678a44c4 +-t samtools_rmdup --tool-version 586f9e1cdb2b +-t modify_loom --tool-version 05631436cdf1 +-t scater_plot_tsne --tool-version 99f912d5af9f +-t salmon_kallisto_mtx_to_10x --tool-version 88f5a0a6a818 +-t salmon_kallisto_mtx_to_10x --tool-version e42c217a450f +-t scanpy_find_cluster --tool-version 35caf3c27c91 +-t scanpy_find_cluster --tool-version 9e4f79e40b84 +-t reshape2_melt --tool-version 317ed0ee8bf2 +-t freebayes --tool-version ef2c525bd8cd +-t bcftools_cnv --tool-version 01d6b7d6365e +-t bcftools_roh --tool-version b76adb2f1c51 +-t vcfbedintersect --tool-version aea8e90ad788 +-t vcfvcfintersect --tool-version 166c4f50525f diff --git a/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/0819d429057bf8a0.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/0819d429057bf8a0.json new file mode 100644 index 000000000..ee80f2c60 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/0819d429057bf8a0.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "0819d429057bf8a0", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:37:45.221392", + "update_time": "2024-09-01T06:38:28.699590", + "galaxy_version": "24.1", + "external_id": "gxy-pbdpw", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/50/registry.xml' '/galaxy/server/database/jobs_directory/000/50/upload_params.json' '90:/galaxy/server/database/objects/3/9/b/dataset_39b5701b-fdbb-480d-9ae1-1010362d4e08_files:/galaxy/server/database/objects/3/9/b/dataset_39b5701b-fdbb-480d-9ae1-1010362d4e08.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_vheq472g\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"bamtools.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_z3od3c0g\", \"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": "423320a086027da1", + "src": "hda", + "uuid": "39b5701b-fdbb-480d-9ae1-1010362d4e08" + } + }, + "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-24-09-01-06-11-1/errors/0fdb98639d6d499e.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/0fdb98639d6d499e.json new file mode 100644 index 000000000..2279dbbaf --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/0fdb98639d6d499e.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "0fdb98639d6d499e", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T07:17:14.830621", + "update_time": "2024-09-01T07:17:26.757203", + "galaxy_version": "24.1", + "external_id": "gxy-qm7kb", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/278/registry.xml' '/galaxy/server/database/jobs_directory/000/278/upload_params.json' '370:/galaxy/server/database/objects/5/f/8/dataset_5f8ddfa1-cb26-4898-88bf-94f97b7ee950_files:/galaxy/server/database/objects/5/f/8/dataset_5f8ddfa1-cb26-4898-88bf-94f97b7ee950.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_bz7l20r8\"", + "files_metadata": "{\"__current_case__\": 342, \"file_type\": \"vcf\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"cnv.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_okb05zx6\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"vcf\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "c399144c33efb331", + "src": "hda", + "uuid": "5f8ddfa1-cb26-4898-88bf-94f97b7ee950" + } + }, + "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-24-09-01-06-11-1/errors/15b628f3a8b45d2c.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/15b628f3a8b45d2c.json new file mode 100644 index 000000000..9731f24e7 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/15b628f3a8b45d2c.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "15b628f3a8b45d2c", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:52:17.979200", + "update_time": "2024-09-01T06:55:00.198902", + "galaxy_version": "24.1", + "external_id": "gxy-jwpk2", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/201/registry.xml' '/galaxy/server/database/jobs_directory/000/201/upload_params.json' '266:/galaxy/server/database/objects/a/c/1/dataset_ac145c97-0ccc-4734-af6b-7098b1ca253c_files:/galaxy/server/database/objects/a/c/1/dataset_ac145c97-0ccc-4734-af6b-7098b1ca253c.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_vzyore6w\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"samtools_flagstat.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_4_1uwcxt\", \"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": "bd7bdbfc10eca8c1", + "src": "hda", + "uuid": "ac145c97-0ccc-4734-af6b-7098b1ca253c" + } + }, + "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-24-09-01-06-11-1/errors/17b9af32bdd92c3c.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/17b9af32bdd92c3c.json new file mode 100644 index 000000000..e28dc2e79 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/17b9af32bdd92c3c.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "17b9af32bdd92c3c", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:43:40.568049", + "update_time": "2024-09-01T06:45:24.125923", + "galaxy_version": "24.1", + "external_id": "gxy-b5r4g", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/109/registry.xml' '/galaxy/server/database/jobs_directory/000/109/upload_params.json' '162:/galaxy/server/database/objects/8/4/3/dataset_8437b923-4ebe-4dff-ae17-b6dd10e8ed7c_files:/galaxy/server/database/objects/8/4/3/dataset_8437b923-4ebe-4dff-ae17-b6dd10e8ed7c.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_mdcx2kdw\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"macs_2.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_p_ysy_af\", \"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": "92bca07b031c2570", + "src": "hda", + "uuid": "8437b923-4ebe-4dff-ae17-b6dd10e8ed7c" + } + }, + "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-24-09-01-06-11-1/errors/1e422eebd2ee4ea3.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/1e422eebd2ee4ea3.json new file mode 100644 index 000000000..bd8a7530d --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/1e422eebd2ee4ea3.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "1e422eebd2ee4ea3", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:37:11.179031", + "update_time": "2024-09-01T06:37:25.861255", + "galaxy_version": "24.1", + "external_id": "gxy-cm75z", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/39/registry.xml' '/galaxy/server/database/jobs_directory/000/39/upload_params.json' '79:/galaxy/server/database/objects/f/1/8/dataset_f180f2b2-c876-4fe7-b874-6db5e5943931_files:/galaxy/server/database/objects/f/1/8/dataset_f180f2b2-c876-4fe7-b874-6db5e5943931.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_19qb3rz1\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"hisat2_1.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_vu_bmosp\", \"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": "24ad2c9072f75fb5", + "src": "hda", + "uuid": "f180f2b2-c876-4fe7-b874-6db5e5943931" + } + }, + "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-24-09-01-06-11-1/errors/1ed84d616d66eb3e.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/1ed84d616d66eb3e.json new file mode 100644 index 000000000..d43738848 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/1ed84d616d66eb3e.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "1ed84d616d66eb3e", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:43:05.343824", + "update_time": "2024-09-01T06:43:22.413583", + "galaxy_version": "24.1", + "external_id": "gxy-jfgnc", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/89/registry.xml' '/galaxy/server/database/jobs_directory/000/89/upload_params.json' '142:/galaxy/server/database/objects/a/5/9/dataset_a5965c51-d117-4112-9a2a-63efb66ca432_files:/galaxy/server/database/objects/a/5/9/dataset_a5965c51-d117-4112-9a2a-63efb66ca432.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_ialiy06c\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"fastp1.json.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_arhv8cn_\", \"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": "cfdbc492c480829d", + "src": "hda", + "uuid": "a5965c51-d117-4112-9a2a-63efb66ca432" + } + }, + "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-24-09-01-06-11-1/errors/28e6fe619e9e1c2d.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/28e6fe619e9e1c2d.json new file mode 100644 index 000000000..0db8e9cb5 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/28e6fe619e9e1c2d.json @@ -0,0 +1,56 @@ +{ + "model_class": "Job", + "id": "28e6fe619e9e1c2d", + "history_id": "0f5f5d39c9be041a", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T07:12:12.934841", + "update_time": "2024-09-01T07:12:18.837353", + "galaxy_version": "24.1", + "external_id": "gxy-57kmf", + "handler": null, + "job_runner_name": null, + "command_line": "ln -s -f '/galaxy/server/database/objects/5/4/0/dataset_54058f86-0e55-4242-8e7c-69e29d989e47.dat' 'localref.fa' && samtools faidx 'localref.fa' 2>&1 || echo \"Error running samtools faidx for FreeBayes\" >&2 && ln -s -f '/galaxy/server/database/objects/9/1/9/dataset_9196fc04-b291-4934-9ca7-95edcbf7aa6d.dat' 'b_0.bam' && ln -s -f '/galaxy/server/database/objects/_metadata_files/0/8/c/metadata_08ceb78f-5a73-48fa-a0a1-d6361e1ca94b.dat' 'b_0.bam.bai' && samtools view -H b_0.bam| grep '^@SQ' | cut -f 2- | awk '{ gsub(\"^SN:\",\"\",$1); gsub(\"^LN:\",\"\",$2); print $1\"\\t0\\t\"$2; }' >> regions_all.bed && sort -u regions_all.bed > regions_uniq.bed && mkdir vcf_output failed_alleles trace && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do echo \" freebayes --region '$i' --bam 'b_0.bam' --fasta-reference 'localref.fa' --vcf './vcf_output/part_$i.vcf' --min-coverage 14 --skip-coverage 0 --limit-coverage 0 --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0.05 --pooled-continuous --report-monomorphic --standard-filters \"; done > freebayes_commands.sh && cat freebayes_commands.sh | parallel --will-cite -j ${GALAXY_SLOTS:-1} && grep \"^#\" \"./vcf_output/part_$i.vcf\" > header.txt && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do cat \"./vcf_output/part_$i.vcf\" | grep -v \"^#\" || true ; done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '/galaxy/server/database/objects/1/3/1/dataset_13188573-d0df-4046-b4a6-2da6796dbc9f.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"bam\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "options_type": "{\"__current_case__\": 4, \"options_type_selector\": \"naive_w_filters\"}", + "coverage_options": "{\"__current_case__\": 0, \"coverage_options_selector\": \"set\", \"limit_coverage\": \"0\", \"min_coverage\": \"14\", \"skip_coverage\": \"0\"}", + "target_limit_type": "{\"__current_case__\": 0, \"target_limit_type_selector\": \"do_not_limit\"}", + "reference_source": "{\"__current_case__\": 1, \"batchmode\": {\"__current_case__\": 0, \"input_bams\": {\"values\": [{\"id\": 345, \"src\": \"hda\"}]}, \"processmode\": \"individual\"}, \"ref_file\": {\"values\": [{\"id\": 346, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}" + }, + "inputs": { + "reference_source|ref_file": { + "id": "77e464c82d2dd442", + "src": "hda", + "uuid": "54058f86-0e55-4242-8e7c-69e29d989e47" + }, + "reference_source|batchmode|input_bams": { + "id": "cd7534d53f3302d3", + "src": "hda", + "uuid": "9196fc04-b291-4934-9ca7-95edcbf7aa6d" + } + }, + "outputs": { + "output_vcf": { + "id": "0d42b19d3e5ce231", + "src": "hda", + "uuid": "13188573-d0df-4046-b4a6-2da6796dbc9f" + } + }, + "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-24-09-01-06-11-1/errors/2a40b2de8c94c1df.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/2a40b2de8c94c1df.json new file mode 100644 index 000000000..cf8a1b579 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/2a40b2de8c94c1df.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "2a40b2de8c94c1df", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T07:21:19.408953", + "update_time": "2024-09-01T07:21:31.824479", + "galaxy_version": "24.1", + "external_id": "gxy-mhtnh", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/294/registry.xml' '/galaxy/server/database/jobs_directory/000/294/upload_params.json' '389:/galaxy/server/database/objects/6/d/2/dataset_6d210276-ecec-4df9-bdb6-f9affd673aea_files:/galaxy/server/database/objects/6/d/2/dataset_6d210276-ecec-4df9-bdb6-f9affd673aea.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_esvzkvee\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"vcfvcfintersect-input1.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_bcgzvdqf\", \"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": "a4c10fbd940a1cdd", + "src": "hda", + "uuid": "6d210276-ecec-4df9-bdb6-f9affd673aea" + } + }, + "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-24-09-01-06-11-1/errors/2ebb3ad5094e871e.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/2ebb3ad5094e871e.json new file mode 100644 index 000000000..5505554dd --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/2ebb3ad5094e871e.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "2ebb3ad5094e871e", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:43:07.112440", + "update_time": "2024-09-01T06:43:23.098087", + "galaxy_version": "24.1", + "external_id": "gxy-cdftb", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/94/registry.xml' '/galaxy/server/database/jobs_directory/000/94/upload_params.json' '147:/galaxy/server/database/objects/4/e/6/dataset_4e6e407e-e786-42b2-aefa-c356c976cb1d_files:/galaxy/server/database/objects/4/e/6/dataset_4e6e407e-e786-42b2-aefa-c356c976cb1d.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_1qo0_c7r\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"slamdunk_summary.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_x_ko4_kv\", \"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": "713a6342e499a9bf", + "src": "hda", + "uuid": "4e6e407e-e786-42b2-aefa-c356c976cb1d" + } + }, + "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-24-09-01-06-11-1/errors/2fe69f8fdae96ff9.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/2fe69f8fdae96ff9.json new file mode 100644 index 000000000..8a662516e --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/2fe69f8fdae96ff9.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "2fe69f8fdae96ff9", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:43:38.293368", + "update_time": "2024-09-01T06:44:14.368302", + "galaxy_version": "24.1", + "external_id": "gxy-68sx8", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/101/registry.xml' '/galaxy/server/database/jobs_directory/000/101/upload_params.json' '154:/galaxy/server/database/objects/f/9/2/dataset_f92d5827-0628-4e3e-abec-05ad7bfd91e0_files:/galaxy/server/database/objects/f/9/2/dataset_f92d5827-0628-4e3e-abec-05ad7bfd91e0.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_5tq61rg8\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"bowtie2_2.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ycl9z06x\", \"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": "d5242c50cab41bb4", + "src": "hda", + "uuid": "f92d5827-0628-4e3e-abec-05ad7bfd91e0" + } + }, + "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-24-09-01-06-11-1/errors/2ff7fac60df81cb9.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/2ff7fac60df81cb9.json new file mode 100644 index 000000000..2ac71eae9 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/2ff7fac60df81cb9.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "2ff7fac60df81cb9", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:49:49.286405", + "update_time": "2024-09-01T06:50:06.920424", + "galaxy_version": "24.1", + "external_id": "gxy-nnlc5", + "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' '218:/galaxy/server/database/objects/d/2/a/dataset_d2ad9297-a35b-4e37-9167-cd8197f34e51_files:/galaxy/server/database/objects/d/2/a/dataset_d2ad9297-a35b-4e37-9167-cd8197f34e51.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_h9pf87do\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"fastqc_1.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data__21extf8\", \"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": "de0733c10db19348", + "src": "hda", + "uuid": "d2ad9297-a35b-4e37-9167-cd8197f34e51" + } + }, + "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-24-09-01-06-11-1/errors/3efcd2344b65bd51.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/3efcd2344b65bd51.json new file mode 100644 index 000000000..dbc44990a --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/3efcd2344b65bd51.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "3efcd2344b65bd51", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:37:12.025565", + "update_time": "2024-09-01T06:38:15.222390", + "galaxy_version": "24.1", + "external_id": "gxy-qcg74", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/42/registry.xml' '/galaxy/server/database/jobs_directory/000/42/upload_params.json' '82:/galaxy/server/database/objects/d/3/f/dataset_d3f0f219-a695-46ab-b04b-1b9d8acdf835_files:/galaxy/server/database/objects/d/3/f/dataset_d3f0f219-a695-46ab-b04b-1b9d8acdf835.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_tdv1fbap\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"hicexplorer2.log\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_5fzma_w7\", \"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": "f65897791ea16e04", + "src": "hda", + "uuid": "d3f0f219-a695-46ab-b04b-1b9d8acdf835" + } + }, + "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-24-09-01-06-11-1/errors/452f1202fd627b61.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/452f1202fd627b61.json new file mode 100644 index 000000000..a89aa0603 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/452f1202fd627b61.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "452f1202fd627b61", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T07:19:36.743667", + "update_time": "2024-09-01T07:19:50.039800", + "galaxy_version": "24.1", + "external_id": "gxy-wbkqb", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/286/registry.xml' '/galaxy/server/database/jobs_directory/000/286/upload_params.json' '381:/galaxy/server/database/objects/6/f/2/dataset_6f20d137-fc77-4ddd-baf8-36ec00e78ca4_files:/galaxy/server/database/objects/6/f/2/dataset_6f20d137-fc77-4ddd-baf8-36ec00e78ca4.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_tllmrwid\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"vcflib.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_a1m9pc_j\", \"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": "492ff6af1aa3ce84", + "src": "hda", + "uuid": "6f20d137-fc77-4ddd-baf8-36ec00e78ca4" + } + }, + "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-24-09-01-06-11-1/errors/489a622667d2a7f4.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/489a622667d2a7f4.json new file mode 100644 index 000000000..066cb95b9 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/489a622667d2a7f4.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "489a622667d2a7f4", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:47:46.555992", + "update_time": "2024-09-01T06:47:58.485936", + "galaxy_version": "24.1", + "external_id": "gxy-xgqks", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/144/registry.xml' '/galaxy/server/database/jobs_directory/000/144/upload_params.json' '197:/galaxy/server/database/objects/9/c/b/dataset_9cb7b44a-1052-4d06-adaa-281dcf3f3e7c_files:/galaxy/server/database/objects/9/c/b/dataset_9cb7b44a-1052-4d06-adaa-281dcf3f3e7c.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_2jun9aq4\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"cc_wt15.bpc.tab\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_8bfm07x2\", \"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": "2d6a0001f982f1a4", + "src": "hda", + "uuid": "9cb7b44a-1052-4d06-adaa-281dcf3f3e7c" + } + }, + "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-24-09-01-06-11-1/errors/4b5dad8e931c522a.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/4b5dad8e931c522a.json new file mode 100644 index 000000000..298396e00 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/4b5dad8e931c522a.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "4b5dad8e931c522a", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T07:09:22.096746", + "update_time": "2024-09-01T07:09:34.411286", + "galaxy_version": "24.1", + "external_id": "gxy-f5mz9", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/248/registry.xml' '/galaxy/server/database/jobs_directory/000/248/upload_params.json' '338:/galaxy/server/database/objects/6/e/1/dataset_6e100300-f136-4e0c-b9c4-5536ba9239d8_files:/galaxy/server/database/objects/6/e/1/dataset_6e100300-f136-4e0c-b9c4-5536ba9239d8.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_5mmpyfsq\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"addtest.loom\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_r9fym_kf\", \"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": "c6d07d010376b33c", + "src": "hda", + "uuid": "6e100300-f136-4e0c-b9c4-5536ba9239d8" + } + }, + "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-24-09-01-06-11-1/errors/5757eb3d49d1b901.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/5757eb3d49d1b901.json new file mode 100644 index 000000000..e6efe58c5 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/5757eb3d49d1b901.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "5757eb3d49d1b901", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:37:51.029672", + "update_time": "2024-09-01T06:41:01.908230", + "galaxy_version": "24.1", + "external_id": "gxy-xpfnv", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/68/registry.xml' '/galaxy/server/database/jobs_directory/000/68/upload_params.json' '108:/galaxy/server/database/objects/7/b/f/dataset_7bf98ce0-aca1-43a0-a883-ee10dfcff2f2_files:/galaxy/server/database/objects/7/b/f/dataset_7bf98ce0-aca1-43a0-a883-ee10dfcff2f2.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_7z4vzb3p\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"picard_CollectAlignmentSummaryMetrics.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_wim76u4h\", \"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": "ae065cc28c8db632", + "src": "hda", + "uuid": "7bf98ce0-aca1-43a0-a883-ee10dfcff2f2" + } + }, + "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-24-09-01-06-11-1/errors/581ba2a7c02bc8c2.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/581ba2a7c02bc8c2.json new file mode 100644 index 000000000..f7d5c82b8 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/581ba2a7c02bc8c2.json @@ -0,0 +1,51 @@ +{ + "model_class": "Job", + "id": "581ba2a7c02bc8c2", + "history_id": "0f5f5d39c9be041a", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T07:19:24.218176", + "update_time": "2024-09-01T07:19:35.013378", + "galaxy_version": "24.1", + "external_id": "gxy-7hsq2", + "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/7/d/d/dataset_7ddd3cd7-be45-4a5a-919f-c925bdceb389.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools roh --AF-dflt \"0.4\" --GTs-only \"30.0\" --hw-to-az \"6.7e-08\" --az-to-hw \"5e-09\" --output-type r input.vcf.gz > '/galaxy/server/database/objects/b/0/9/dataset_b09e8e45-4aa5-4fea-8cff-63e68640ab3e.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"vcf\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "output_type": "\"r\"", + "sec_hmm": "{\"az_to_hw\": \"5e-09\", \"hw_to_az\": \"6.7e-08\", \"viterbi_training\": false}", + "sec_general": "{\"AF_dflt\": \"0.4\", \"AF_file\": null, \"AF_tag\": \"\", \"GTs_only\": \"30.0\", \"buffer_overlap\": \"\", \"buffer_size\": \"\", \"estimate_AF\": null, \"genetic_map\": null, \"rec_rate\": \"\", \"sample\": null, \"skip_indels\": false}", + "sec_restrict": "{\"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_file": { + "id": "ead7bf0d85458c3d", + "src": "hda", + "uuid": "7ddd3cd7-be45-4a5a-919f-c925bdceb389" + } + }, + "outputs": { + "output_file": { + "id": "8e3b6fdd7858e3d3", + "src": "hda", + "uuid": "b09e8e45-4aa5-4fea-8cff-63e68640ab3e" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "Number of target samples: 1\nNumber of --estimate-AF samples: 0\nNumber of sites in the buffer/overlap: unlimited\nNumber of lines total/processed: 8890/8888\nNumber of lines filtered/no AF/not biallelic/dup: 0/0/1/1\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "Number of target samples: 1\nNumber of --estimate-AF samples: 0\nNumber of sites in the buffer/overlap: unlimited\nNumber of lines total/processed: 8890/8888\nNumber of lines filtered/no AF/not biallelic/dup: 0/0/1/1\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/653676bc098c5fdb.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/653676bc098c5fdb.json new file mode 100644 index 000000000..0bbe58165 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/653676bc098c5fdb.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "653676bc098c5fdb", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:44:40.503638", + "update_time": "2024-09-01T06:47:45.748373", + "galaxy_version": "24.1", + "external_id": "gxy-ftgp9", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/130/registry.xml' '/galaxy/server/database/jobs_directory/000/130/upload_params.json' 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--region '$i' --bam 'b_0.bam' --fasta-reference 'localref.fa' --vcf './vcf_output/part_$i.vcf' --min-coverage 0 --skip-coverage 0 --limit-coverage 400 \"; done > freebayes_commands.sh && cat freebayes_commands.sh | parallel --will-cite -j ${GALAXY_SLOTS:-1} && grep \"^#\" \"./vcf_output/part_$i.vcf\" > header.txt && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do cat \"./vcf_output/part_$i.vcf\" | grep -v \"^#\" || true ; done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '/galaxy/server/database/objects/f/a/6/dataset_fa616baa-d4f1-4b84-812b-14a39e432fab.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"bam\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "options_type": "{\"__current_case__\": 1, \"options_type_selector\": \"simple\"}", + "coverage_options": "{\"__current_case__\": 0, \"coverage_options_selector\": \"set\", \"limit_coverage\": \"400\", \"min_coverage\": \"0\", \"skip_coverage\": \"0\"}", + "target_limit_type": "{\"__current_case__\": 0, \"target_limit_type_selector\": \"do_not_limit\"}", + "reference_source": "{\"__current_case__\": 1, \"batchmode\": {\"__current_case__\": 0, \"input_bams\": {\"values\": [{\"id\": 357, \"src\": \"hda\"}]}, \"processmode\": \"individual\"}, \"ref_file\": {\"values\": [{\"id\": 358, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}" + }, + "inputs": { + "reference_source|ref_file": { + "id": "0717868957076543", + "src": "hda", + "uuid": "e8102b39-4eae-4c3f-b03d-c40a3fcebc2b" + }, + "reference_source|batchmode|input_bams": { + "id": "86ac0b829e0ede78", + "src": "hda", + "uuid": "d8497632-be86-4cd4-9002-38bed82e337e" + } + }, + "outputs": { + "output_vcf": { + "id": "0f32c5a94b839107", + "src": "hda", + "uuid": "fa616baa-d4f1-4b84-812b-14a39e432fab" + } + }, + "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-24-09-01-06-11-1/errors/d69fe4bde36ad371.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/d69fe4bde36ad371.json new file mode 100644 index 000000000..8e7d34e7a --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/d69fe4bde36ad371.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "d69fe4bde36ad371", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:44:38.434004", + "update_time": "2024-09-01T06:47:45.612940", + "galaxy_version": "24.1", + "external_id": "gxy-qwt9n", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/123/registry.xml' 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"hda", + "uuid": "525c73b2-dfd5-4787-b9f5-dd9e47d5f462" + } + }, + "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-24-09-01-06-11-1/errors/d88f6a5fa816379a.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/d88f6a5fa816379a.json new file mode 100644 index 000000000..140920d1d --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/d88f6a5fa816379a.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "d88f6a5fa816379a", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:37:10.905497", + "update_time": "2024-09-01T06:37:27.241183", + "galaxy_version": "24.1", + "external_id": "gxy-vk6jk", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/38/registry.xml' '/galaxy/server/database/jobs_directory/000/38/upload_params.json' '78:/galaxy/server/database/objects/c/f/2/dataset_cf25a3f9-9936-4ccc-9a4a-c151489d6d44_files:/galaxy/server/database/objects/c/f/2/dataset_cf25a3f9-9936-4ccc-9a4a-c151489d6d44.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_7da0usgk\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"bowtie2_2.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_0mcz268m\", \"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": "8d3d755701c966f7", + "src": "hda", + "uuid": "cf25a3f9-9936-4ccc-9a4a-c151489d6d44" + } + }, + "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-24-09-01-06-11-1/errors/d90f49ab235eaae5.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/d90f49ab235eaae5.json new file mode 100644 index 000000000..5220a93c6 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/d90f49ab235eaae5.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "d90f49ab235eaae5", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": 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\"/galaxy/server/database/tmp/upload_file_data_svbwmeh_\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", + "file_count": "\"auto\"", + "file_type": "\"vcf\"" + }, + "inputs": {}, + "outputs": { + "output0": { + "id": "51b2eb6460eb99a0", + "src": "hda", + "uuid": "3e5945c0-507d-4caf-9e27-99f4c2d3199a" + } + }, + "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-24-09-01-06-11-1/errors/e73af671a892f31c.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/e73af671a892f31c.json new file mode 100644 index 000000000..8b58c32ab --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/e73af671a892f31c.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "e73af671a892f31c", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:43:07.707581", + "update_time": "2024-09-01T06:43:23.550786", + "galaxy_version": "24.1", + "external_id": "gxy-zqk2q", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/96/registry.xml' '/galaxy/server/database/jobs_directory/000/96/upload_params.json' '149:/galaxy/server/database/objects/3/7/a/dataset_37a7feb7-b565-43b9-8ff5-b7e1bad1a83f_files:/galaxy/server/database/objects/3/7/a/dataset_37a7feb7-b565-43b9-8ff5-b7e1bad1a83f.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_9y_lo3fo\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": 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b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/fc7e18a9a612ec6a.json new file mode 100644 index 000000000..cdaab11cc --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/errors/fc7e18a9a612ec6a.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "fc7e18a9a612ec6a", + "history_id": "0f5f5d39c9be041a", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-01T06:37:50.466647", + "update_time": "2024-09-01T06:41:01.545131", + "galaxy_version": "24.1", + "external_id": "gxy-wzhgh", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/66/registry.xml' '/galaxy/server/database/jobs_directory/000/66/upload_params.json' 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2024-09-01T07:21:03.335210 upload1 +ae9d5c9f144658d3 ok 2024-09-01T07:21:03.294286 upload1 +1dc43afa8922e2b5 ok 2024-09-01T07:21:02.237879 upload1 +492876b2b8d7fa19 ok 2024-09-01T07:20:33.786659 toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc3+galaxy0 +b73db2180733969f ok 2024-09-01T07:20:12.580572 upload1 +06416ac3afaea875 ok 2024-09-01T07:19:59.434447 upload1 +452f1202fd627b61 error 2024-09-01T07:19:50.039800 upload1 +581ba2a7c02bc8c2 error 2024-09-01T07:19:35.013378 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10 +beb54766a4897cd4 ok 2024-09-01T07:19:24.061817 upload1 +d90f49ab235eaae5 error 2024-09-01T07:19:02.072921 upload1 +4789a0dc3a906884 ok 2024-09-01T07:18:48.340886 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10 +c10a472e563afa0b ok 2024-09-01T07:18:32.074647 upload1 +a663cbdc2ddcf8b2 ok 2024-09-01T07:18:08.949693 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10 +d7991a0e2a2ce0d7 ok 2024-09-01T07:17:49.446849 upload1 +0fdb98639d6d499e error 2024-09-01T07:17:26.757203 upload1 +8a0841f2935fbf4b ok 2024-09-01T07:17:14.096526 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10 +9daec2bfe02db058 ok 2024-09-01T07:16:34.815317 upload1 +327188afff1e1a3d ok 2024-09-01T07:16:11.431491 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0 +9568984c6aaa2a59 ok 2024-09-01T07:15:55.613736 upload1 +82cc754c1d951f3b ok 2024-09-01T07:15:55.512176 upload1 +8ae0eb027da1835a ok 2024-09-01T07:15:31.961460 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0 +0a6fdadd6c20517d ok 2024-09-01T07:15:15.817218 upload1 +fd640c1837446b76 ok 2024-09-01T07:15:15.024034 upload1 +d52dd58fbb5ccf5d error 2024-09-01T07:14:51.268678 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0 +e66e7308b576252b ok 2024-09-01T07:14:44.987348 upload1 +4f917c95c8c5722b ok 2024-09-01T07:14:44.083994 upload1 +bd7bdbfc10eca8c1 ok 2024-09-01T07:14:20.020704 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0 +8237a51c6718f087 ok 2024-09-01T07:14:03.620217 upload1 +82ef9543acfff0c4 ok 2024-09-01T07:14:03.609901 upload1 +284dbc4a3c716da8 ok 2024-09-01T07:13:39.516039 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0 +8ab69bd1ebf5f0b7 ok 2024-09-01T07:13:23.725269 upload1 +1debb088acd9df69 ok 2024-09-01T07:13:22.797146 upload1 +77bb97717ea8b08c ok 2024-09-01T07:12:59.772999 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0 +61f3283ae8dcedc4 ok 2024-09-01T07:12:43.226301 upload1 +a65cedc55b6806df ok 2024-09-01T07:12:42.195058 upload1 +28e6fe619e9e1c2d error 2024-09-01T07:12:18.837353 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0 +1ae8b779ba3b085f ok 2024-09-01T07:12:12.576354 upload1 +ce4678e091ca07c2 ok 2024-09-01T07:12:11.591773 upload1 +3ccef5de04c0d2f2 ok 2024-09-01T07:11:48.753538 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0 +02aa3c389f0c2a28 ok 2024-09-01T07:11:25.039258 upload1 +1042e89d98f78119 ok 2024-09-01T07:11:23.889774 upload1 +42daffbed2986754 ok 2024-09-01T07:10:54.740789 toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_tsne/scater_plot_tsne/1.22.0 +762cc63df7c7f51c ok 2024-09-01T07:09:58.156966 upload1 +ac9f93a41bc64e57 ok 2024-09-01T07:09:44.913605 upload1 +4b5dad8e931c522a error 2024-09-01T07:09:34.411286 upload1 +5063297f6a58e93c ok 2024-09-01T07:09:21.161368 toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1 +24cce3b5e7e7fa13 ok 2024-09-01T07:09:03.664530 upload1 +9e6b374bbaf897c5 ok 2024-09-01T07:09:03.616666 upload1 +8d7aaf7f3ff83e96 ok 2024-09-01T07:08:39.803002 toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1 +0db4474538886841 ok 2024-09-01T07:08:12.684487 upload1 +9d3848d5ec756b25 ok 2024-09-01T07:08:12.666694 upload1 +e68db0c123581860 ok 2024-09-01T07:07:47.047852 toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 +8bf3d520ef99b782 ok 2024-09-01T07:07:29.905835 upload1 +08f780b405856407 ok 2024-09-01T07:07:04.998903 toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9 +9c37d9638ae8e73c ok 2024-09-01T07:06:48.972316 upload1 +639ae6166a3981e6 ok 2024-09-01T07:06:48.004368 upload1 +5ba71dacf52e38d8 ok 2024-09-01T07:06:33.434521 upload1 +cdb8918ea01b68fe error 2024-09-01T07:06:23.434392 upload1 +d5bd1ac7a2a49447 ok 2024-09-01T07:06:09.649067 toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9 +26c31b38edc0d1f6 ok 2024-09-01T07:05:54.414423 upload1 +923965d480e74ad0 ok 2024-09-01T07:05:30.113438 toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.9 +0d1d911a66d03240 ok 2024-09-01T07:05:12.635719 upload1 +9b02e5e1ea4c43a4 ok 2024-09-01T07:05:11.838637 upload1 +79a8cb67eecad806 ok 2024-09-01T07:04:46.397720 toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.3 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upload1 +c4cb064e29a3e0f7 ok 2024-09-01T07:00:22.382039 toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1 +715846e208c316d2 ok 2024-09-01T06:59:29.475645 upload1 +0d3c5de3e5c91d32 ok 2024-09-01T06:59:02.237909 toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1 +a51f03954997a9af ok 2024-09-01T06:57:58.954657 upload1 +ad76ce97aaa575c4 ok 2024-09-01T06:57:32.908457 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 +0178724df954a766 ok 2024-09-01T06:57:12.633806 upload1 +8221186f614b82c0 ok 2024-09-01T06:56:48.709937 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 +b14c4b460378e2ff ok 2024-09-01T06:56:20.733752 upload1 +e785bde77f6c0c50 ok 2024-09-01T06:56:20.704399 upload1 +b5cf52fddd2eae10 ok 2024-09-01T06:55:55.651219 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 +02653ed4bb020c6f ok 2024-09-01T06:55:35.193087 upload1 +7db6adfcfe2cf88f ok 2024-09-01T06:55:34.233580 upload1 +92545a1804560c88 ok 2024-09-01T06:55:09.940537 upload1 +dfd30aba3999ca69 ok 2024-09-01T06:55:01.210513 upload1 +baf966ba70779e05 ok 2024-09-01T06:55:00.330577 upload1 +15b628f3a8b45d2c error 2024-09-01T06:55:00.198902 upload1 +2d6a0001f982f1a4 ok 2024-09-01T06:54:59.943693 upload1 +f286f16124c23de8 ok 2024-09-01T06:54:59.705991 upload1 +2bb1dd9950422550 ok 2024-09-01T06:54:41.305159 upload1 +e73eb136ea9be59c ok 2024-09-01T06:54:39.744820 upload1 +0d64f6c295ce8f7e ok 2024-09-01T06:54:38.903405 upload1 +ba274a0594c0800e ok 2024-09-01T06:54:38.619734 upload1 +f611a89eb538dbe7 ok 2024-09-01T06:54:20.540053 upload1 +e8daa2f7c7dd4915 ok 2024-09-01T06:54:18.902876 upload1 +872f2e5ae242ac40 ok 2024-09-01T06:54:17.307338 upload1 +ec8f5b48e9d638bc ok 2024-09-01T06:54:17.195993 upload1 +209e8429f8b4cb68 ok 2024-09-01T06:53:59.441831 upload1 +90d7c0f10a86b18f ok 2024-09-01T06:53:56.807788 upload1 +8b35b8ad78bd0b71 ok 2024-09-01T06:53:55.928694 upload1 +b1f32b9c29e7e938 ok 2024-09-01T06:53:55.732203 upload1 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2024-09-01T06:52:06.098429 upload1 +39e42c2980abdec5 ok 2024-09-01T06:51:47.903291 upload1 +9027922c07292920 ok 2024-09-01T06:51:47.716860 upload1 +08a6ae88f4c4b87a ok 2024-09-01T06:51:45.436742 upload1 +e0f27c64b490a921 ok 2024-09-01T06:51:45.406927 upload1 +6814ab32d596238e ok 2024-09-01T06:51:26.825445 upload1 +003c6a3ef8917394 ok 2024-09-01T06:51:26.533260 upload1 +92bca07b031c2570 ok 2024-09-01T06:51:24.351467 upload1 +63b0c07df9cd1a99 ok 2024-09-01T06:51:24.343485 upload1 +5125440fd3c1df6b ok 2024-09-01T06:50:57.654712 upload1 +bc1db3882a7f5450 ok 2024-09-01T06:50:48.376847 upload1 +f8b61482e0416de9 ok 2024-09-01T06:50:47.455231 upload1 +9232ef9a71209bf9 error 2024-09-01T06:50:45.822710 upload1 +4bdd8303114ad210 ok 2024-09-01T06:50:45.421508 upload1 +deab7028f2695d45 ok 2024-09-01T06:50:44.639622 upload1 +ac211ba113838c43 ok 2024-09-01T06:50:27.411382 upload1 +d5242c50cab41bb4 ok 2024-09-01T06:50:27.110444 upload1 +339fc33b9e8f4e2c ok 2024-09-01T06:50:23.924188 upload1 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2024-09-01T06:47:45.748373 upload1 +d69fe4bde36ad371 error 2024-09-01T06:47:45.612940 upload1 +9d8934708e5d0261 ok 2024-09-01T06:47:45.426293 upload1 +da616343dac2543f ok 2024-09-01T06:47:44.156647 upload1 +b6650900a132da8e ok 2024-09-01T06:47:44.124378 upload1 +092bba238028a448 ok 2024-09-01T06:47:24.709707 upload1 +1562c02072c0e7c4 ok 2024-09-01T06:47:23.499157 upload1 +2e579d560efcd06e ok 2024-09-01T06:47:23.296065 upload1 +c4df62fdc7b2ddcd ok 2024-09-01T06:47:05.021919 upload1 +40ec5ad3f0366ce1 ok 2024-09-01T06:47:03.500414 upload1 +a6efb5c0e2a8d841 ok 2024-09-01T06:47:02.633219 upload1 +c336029ab95b1d6f ok 2024-09-01T06:47:02.349394 upload1 +888078f7e2120d98 ok 2024-09-01T06:46:44.212970 upload1 +a53a933f8ff9995c ok 2024-09-01T06:46:42.348529 upload1 +9e67879db7815cd5 ok 2024-09-01T06:46:41.615205 upload1 +9345e787ee1d96bf ok 2024-09-01T06:46:41.213006 upload1 +784cc9d3f6cae10e ok 2024-09-01T06:46:23.404659 upload1 +478bb3776d3c0518 ok 2024-09-01T06:46:21.158139 upload1 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2024-09-01T06:44:34.452407 upload1 +14624cded418b570 ok 2024-09-01T06:44:34.436565 upload1 +2fe69f8fdae96ff9 error 2024-09-01T06:44:14.368302 upload1 +c96f2cdedf839b98 ok 2024-09-01T06:44:04.927486 upload1 +3e86d99c49ee80c6 ok 2024-09-01T06:44:03.472282 upload1 +b9ec5b827b787067 ok 2024-09-01T06:44:03.251530 upload1 +65dee66288f02e29 ok 2024-09-01T06:43:58.929088 upload1 +dd8074a99ecf53aa ok 2024-09-01T06:43:44.998881 upload1 +1253be96fd7774fb ok 2024-09-01T06:43:42.341676 upload1 +423320a086027da1 ok 2024-09-01T06:43:42.205215 upload1 +818bbbc4915da42e ok 2024-09-01T06:43:37.210868 upload1 +e73af671a892f31c error 2024-09-01T06:43:23.550786 upload1 +2ebb3ad5094e871e error 2024-09-01T06:43:23.098087 upload1 +1ed84d616d66eb3e error 2024-09-01T06:43:22.413583 upload1 +90d6c1306b660912 ok 2024-09-01T06:43:03.017996 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 +eb6446f7253befb6 ok 2024-09-01T06:42:42.818516 upload1 +64f98d71bc2bac30 ok 2024-09-01T06:42:18.835735 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 +fd8e73bdb0cd20d3 ok 2024-09-01T06:41:50.572985 upload1 +6facfe386741a1d7 ok 2024-09-01T06:41:49.495271 upload1 +f65897791ea16e04 ok 2024-09-01T06:41:25.559957 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 +2432a19652de1019 ok 2024-09-01T06:41:05.179357 upload1 +550a9e152a6cfe7d ok 2024-09-01T06:41:02.613948 upload1 +97959635f6439e5c ok 2024-09-01T06:41:02.114383 upload1 +5757eb3d49d1b901 error 2024-09-01T06:41:01.908230 upload1 +96378b79f935ff5d error 2024-09-01T06:41:01.724129 upload1 +fc7e18a9a612ec6a error 2024-09-01T06:41:01.545131 upload1 +8fc662fbc6bcde30 ok 2024-09-01T06:41:01.396472 upload1 +24ad2c9072f75fb5 ok 2024-09-01T06:40:48.327042 upload1 +13563aa44c58aeaf ok 2024-09-01T06:40:42.427499 upload1 +4b9d0f9d3bd07264 ok 2024-09-01T06:40:41.526122 upload1 +2129a7217775195d ok 2024-09-01T06:40:40.518589 upload1 +003bb263eeefdeef ok 2024-09-01T06:40:27.434622 upload1 +8d3d755701c966f7 ok 2024-09-01T06:40:21.597515 upload1 +ffc715d6c5d952ed ok 2024-09-01T06:40:20.898569 upload1 +9134d8030585c9b6 ok 2024-09-01T06:40:19.797281 upload1 +b16f60fa4a0293fe ok 2024-09-01T06:40:06.629815 upload1 +7f089f6e9bfa5149 ok 2024-09-01T06:40:00.728695 upload1 +9350901caecda29c ok 2024-09-01T06:39:59.912755 upload1 +4e76c3858ff053da ok 2024-09-01T06:39:58.934679 upload1 +72e23cadb445b1c2 ok 2024-09-01T06:39:45.906004 upload1 +ae1bbe5e4bf76959 ok 2024-09-01T06:39:39.899127 upload1 +6ed5d2b687499014 ok 2024-09-01T06:39:39.132374 upload1 +e9ec43958db94025 ok 2024-09-01T06:39:37.817180 upload1 +24ad18e51b66b35e ok 2024-09-01T06:39:25.419565 upload1 +63fedbc370f6e2b4 ok 2024-09-01T06:39:19.208428 upload1 +3e444b52213641c9 ok 2024-09-01T06:39:18.303553 upload1 +28aa9462084085ea ok 2024-09-01T06:39:16.997271 upload1 +9918673527029bc4 ok 2024-09-01T06:39:04.241581 upload1 +8b425aef486bfe31 ok 2024-09-01T06:38:58.222206 upload1 +46387bc733526dc0 ok 2024-09-01T06:38:57.014597 upload1 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toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 +0220d52bbb525e17 ok 2024-09-01T06:36:02.818174 upload1 +f368a0391184a0bc ok 2024-09-01T06:36:02.672386 upload1 +8ac2c7a3436e3123 ok 2024-09-01T06:36:01.615161 upload1 +c43fa7dd8d328ba8 ok 2024-09-01T06:35:48.744607 upload1 +e78e822db840a4cb ok 2024-09-01T06:35:47.309998 upload1 +fa5de90cc1bc3135 ok 2024-09-01T06:35:47.224623 upload1 +7576055905cbfd53 ok 2024-09-01T06:35:45.246168 upload1 +3e66b905895552ba ok 2024-09-01T06:35:27.697591 upload1 +699aa0be6b718c80 ok 2024-09-01T06:35:26.436310 upload1 +605b9c60d4868ba7 ok 2024-09-01T06:35:26.426022 upload1 +4eb85bd6b7000860 ok 2024-09-01T06:35:24.443912 upload1 +b79312f9873019a0 ok 2024-09-01T06:34:49.685877 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 +e504eb56c1c09b43 ok 2024-09-01T06:34:33.805217 upload1 +79118445a2ae4924 ok 2024-09-01T06:34:10.426681 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 +4f5d07211d88a9c1 ok 2024-09-01T06:33:54.119830 upload1 +c3ae4a450c53f67c ok 2024-09-01T06:33:31.049837 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 +ee80714db48dd321 ok 2024-09-01T06:33:14.940728 upload1 +6b86f185bc26f926 ok 2024-09-01T06:32:50.732849 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 +d407cd50fc80b371 ok 2024-09-01T06:32:34.751933 upload1 +db7aa3e9d708521c ok 2024-09-01T06:32:11.292553 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 +62eb354288db9131 ok 2024-09-01T06:31:55.097913 upload1 +039b04b47906a4fd ok 2024-09-01T06:31:30.908461 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 +747015e71ac9be6d ok 2024-09-01T06:31:15.707216 upload1 +291a07c912f667a1 ok 2024-09-01T06:30:51.314037 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 +7bff4c686fa3fe0d ok 2024-09-01T06:30:35.335409 upload1 +0b8dda5741c86c37 ok 2024-09-01T06:30:10.893688 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0 +65c15b69694655c0 ok 2024-09-01T06:29:54.264265 upload1 +ac9b4d9a06230776 ok 2024-09-01T06:29:54.226465 upload1 +b7124d2765df34d0 ok 2024-09-01T06:29:30.462932 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0 +f4e8f03b50f50385 ok 2024-09-01T06:29:13.566190 upload1 +a6c3c1dd0dbc7064 ok 2024-09-01T06:29:13.559041 upload1 +19bc0e5055a63b46 ok 2024-09-01T06:28:50.538349 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0 +0f5f5d39c9be041a ok 2024-09-01T06:27:44.573368 upload1 +71d0106886a7baee ok 2024-09-01T06:27:44.566306 upload1 diff --git a/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/results.html b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/results.html new file mode 100644 index 000000000..0f2cf9863 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/results.html @@ -0,0 +1,291 @@ + + + + + + + Test Results (powered by Planemo) + + + + + + + + + + +
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+
+
+ + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/results.json b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/results.json new file mode 100644 index 000000000..42c957095 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-01-06-11-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 69, "errors": 21, "failures": 6, "skips": 0}, "tests": [{"id": "bcftools_cnv/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_cnv", "tool_version": "1.10", "test_index": 0, "time_seconds": 61.586369037628174, "inputs": {"input_file": {"src": "hda", "id": "c8c13d631d7f40f5"}}, "job": {"model_class": "Job", "id": "8a0841f2935fbf4b", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T07:16:35.144694", "update_time": "2024-09-01T07:17:14.096526", "galaxy_version": "24.1", "external_id": "gxy-zqmdv", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/2/6/b/dataset_26bd98b5-3a6b-4386-a31e-3361d095a7fc.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools cnv --output-dir cnv_tmp -p 0 --aberrant \"1.0,1.0\" --BAF-weight 1.0 --BAF-dev \"0.04,0.04\" --LRR-weight 0.2 --LRR-dev \"0.2,0.2\" --LRR-smooth-win 10 --same-prob 0.5 --err-prob 0.0001 --xy-prob 1e-09 input.vcf.gz && mv cnv_tmp/cn.*.tab '/galaxy/server/database/objects/4/9/f/dataset_49f88c42-7e11-492b-ba2e-71462f6895d4.dat' && mv cnv_tmp/summary.*.tab '/galaxy/server/database/objects/e/9/a/dataset_e9abea39-7d40-44d5-819d-86a86d55d85b.dat' && (echo 'Copy-number variation plots (bcftools cnv)' > /galaxy/server/database/objects/2/a/9/dataset_2a91f482-1ba4-427f-a458-f036c95140d2.dat; for plot in cnv_tmp/*.png; do [ -f \"$plot\" ] || break; echo '
> /galaxy/server/database/objects/2/a/9/dataset_2a91f482-1ba4-427f-a458-f036c95140d2.dat; python -m base64 $plot >> /galaxy/server/database/objects/2/a/9/dataset_2a91f482-1ba4-427f-a458-f036c95140d2.dat; echo '\" />
' >> /galaxy/server/database/objects/2/a/9/dataset_2a91f482-1ba4-427f-a458-f036c95140d2.dat; done; echo '' >> /galaxy/server/database/objects/2/a/9/dataset_2a91f482-1ba4-427f-a458-f036c95140d2.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_hmm": "{\"aberrant_control\": \"1.0\", \"aberrant_optimization\": {\"__current_case__\": 0, \"do_optimize\": \"no\"}, \"aberrant_query\": \"1.0\", \"err_prob\": \"0.0001\", \"same_prob\": \"0.5\", \"score_usage\": {\"__current_case__\": 0, \"baf_dev_control\": \"0.04\", \"baf_dev_query\": \"0.04\", \"baf_weight\": \"1.0\", \"compute_on\": \"baf+lrr\", \"lrr_dev_control\": \"0.2\", \"lrr_dev_query\": \"0.2\", \"lrr_smooth_win\": \"10\", \"lrr_weight\": \"0.2\"}, \"xy_prob\": \"1e-09\"}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}", "plotting": "{\"__current_case__\": 0, \"generate_plots\": \"all\", \"plot_threshold\": \"0\"}", "AF_file": null, "control_sample": null, "query_sample": null}, "inputs": {"input_file": {"id": "c8c13d631d7f40f5", "src": "hda", "uuid": "26bd98b5-3a6b-4386-a31e-3361d095a7fc"}}, "outputs": {"output_plots": {"id": "2ce4cbe5e01fd192", "src": "hda", "uuid": "2a91f482-1ba4-427f-a458-f036c95140d2"}, "output_summary": {"id": "5d85f239c8b0af69", "src": "hda", "uuid": "e9abea39-7d40-44d5-819d-86a86d55d85b"}, "output_cn": {"id": "a02510fd887aea95", "src": "hda", "uuid": "49f88c42-7e11-492b-ba2e-71462f6895d4"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of lines: total/processed: 184/184\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Number of lines: total/processed: 184/184\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": "2024-09-01 07:16:55", "plugin": "core", "name": "end_epoch", "raw_value": "1725175015.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 07:16:51", "plugin": "core", "name": "start_epoch", "raw_value": "1725175011.0000000"}, {"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_cnv/1.10-1", "has_data": true, "data": {"tool_id": "bcftools_cnv", "tool_version": "1.10", "test_index": 1, "time_seconds": 12.57231616973877, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_cnv/1.10-2", "has_data": true, "data": {"tool_id": "bcftools_cnv", "tool_version": "1.10", "test_index": 2, "time_seconds": 42.42044281959534, "inputs": {"input_file": {"src": "hda", "id": "d6f8485a62232518"}, "query_sample": "test", "control_sample": "test"}, "job": {"model_class": "Job", "id": "a663cbdc2ddcf8b2", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T07:17:49.635767", "update_time": "2024-09-01T07:18:08.949693", "galaxy_version": "24.1", "external_id": "gxy-ddf65", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/e/c/4/dataset_ec459150-2f72-4977-bfd3-960c45655d03.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools cnv --output-dir cnv_tmp -c 'test' -s 'test' -p 0 --aberrant \"1.0,1.0\" --BAF-weight 1.0 --BAF-dev \"0.04,0.04\" --LRR-weight 0.2 --LRR-dev \"0.2,0.2\" --LRR-smooth-win 10 --same-prob 0.5 --err-prob 0.0001 --xy-prob 1e-09 input.vcf.gz && mv cnv_tmp/cn.*.tab '/galaxy/server/database/objects/9/4/6/dataset_94646035-ba3f-4b8c-9a10-456337b04a19.dat' && mv cnv_tmp/summary.tab '/galaxy/server/database/objects/7/9/4/dataset_794c0053-72d7-4b19-9719-71f5740c5d9f.dat' && (echo 'Copy-number variation plots (bcftools cnv)' > /galaxy/server/database/objects/a/d/7/dataset_ad7fe19d-dc25-4e84-a9f4-097a774a4871.dat; for plot in cnv_tmp/*.png; do [ -f \"$plot\" ] || break; echo '
> /galaxy/server/database/objects/a/d/7/dataset_ad7fe19d-dc25-4e84-a9f4-097a774a4871.dat; python -m base64 $plot >> /galaxy/server/database/objects/a/d/7/dataset_ad7fe19d-dc25-4e84-a9f4-097a774a4871.dat; echo '\" />
' >> /galaxy/server/database/objects/a/d/7/dataset_ad7fe19d-dc25-4e84-a9f4-097a774a4871.dat; done; echo '' >> /galaxy/server/database/objects/a/d/7/dataset_ad7fe19d-dc25-4e84-a9f4-097a774a4871.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_hmm": "{\"aberrant_control\": \"1.0\", \"aberrant_optimization\": {\"__current_case__\": 0, \"do_optimize\": \"no\"}, \"aberrant_query\": \"1.0\", \"err_prob\": \"0.0001\", \"same_prob\": \"0.5\", \"score_usage\": {\"__current_case__\": 0, \"baf_dev_control\": \"0.04\", \"baf_dev_query\": \"0.04\", \"baf_weight\": \"1.0\", \"compute_on\": \"baf+lrr\", \"lrr_dev_control\": \"0.2\", \"lrr_dev_query\": \"0.2\", \"lrr_smooth_win\": \"10\", \"lrr_weight\": \"0.2\"}, \"xy_prob\": \"1e-09\"}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}", "plotting": "{\"__current_case__\": 0, \"generate_plots\": \"all\", \"plot_threshold\": \"0\"}", "AF_file": null, "control_sample": "\"test\"", "query_sample": "\"test\""}, "inputs": {"input_file": {"id": "d6f8485a62232518", "src": "hda", "uuid": "ec459150-2f72-4977-bfd3-960c45655d03"}}, "outputs": {"output_plots": {"id": "fedbf32a47df4d47", "src": "hda", "uuid": "ad7fe19d-dc25-4e84-a9f4-097a774a4871"}, "output_summary": {"id": "f96111e9adcbd1bd", "src": "hda", "uuid": "794c0053-72d7-4b19-9719-71f5740c5d9f"}, "output_cn": {"id": "09d5b61b6aed4ee6", "src": "hda", "uuid": "94646035-ba3f-4b8c-9a10-456337b04a19"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of lines: total/processed: 184/184\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Number of lines: total/processed: 184/184\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}, {"title": "Job End Time", "value": "2024-09-01 07:17:56", "plugin": "core", "name": "end_epoch", "raw_value": "1725175076.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 07:17:50", "plugin": "core", "name": "start_epoch", "raw_value": "1725175070.0000000"}, {"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_cnv/1.10-3", "has_data": true, "data": {"tool_id": "bcftools_cnv", "tool_version": "1.10", "test_index": 3, "time_seconds": 39.23761034011841, "inputs": {"input_file": {"src": "hda", "id": "5d3e5b9e79d9475f"}, "plotting|generate_plots": "none", "sec_hmm|score_usage|compute_on": "baf"}, "job": {"model_class": "Job", "id": "4789a0dc3a906884", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.10", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T07:18:32.475753", "update_time": "2024-09-01T07:18:48.340886", "galaxy_version": "24.1", "external_id": "gxy-cwb67", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/c/6/d/dataset_c6df21eb-e56a-4c90-b479-3f66e07c24cb.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools cnv --output-dir cnv_tmp --aberrant \"1.0,1.0\" --BAF-weight 1 --BAF-dev \"0.04,0.04\" --LRR-weight 0 --same-prob 0.5 --err-prob 0.0001 --xy-prob 1e-09 input.vcf.gz && mv cnv_tmp/cn.*.tab '/galaxy/server/database/objects/e/a/9/dataset_ea936c28-a559-41bd-a536-37be186894f0.dat' && mv cnv_tmp/summary.*.tab '/galaxy/server/database/objects/0/b/2/dataset_0b29bff0-7608-4968-bf7d-386788940dcb.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_hmm": "{\"aberrant_control\": \"1.0\", \"aberrant_optimization\": {\"__current_case__\": 0, \"do_optimize\": \"no\"}, \"aberrant_query\": \"1.0\", \"err_prob\": \"0.0001\", \"same_prob\": \"0.5\", \"score_usage\": {\"__current_case__\": 1, \"baf_dev_control\": \"0.04\", \"baf_dev_query\": \"0.04\", \"baf_weight\": \"1\", \"compute_on\": \"baf\", \"lrr_weight\": \"0\"}, \"xy_prob\": \"1e-09\"}", "sec_restrict": "{\"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}}", "plotting": "{\"__current_case__\": 2, \"generate_plots\": \"none\"}", "AF_file": null, "control_sample": null, "query_sample": null}, "inputs": {"input_file": {"id": "5d3e5b9e79d9475f", "src": "hda", "uuid": "c6df21eb-e56a-4c90-b479-3f66e07c24cb"}}, "outputs": {"output_summary": {"id": "578336aee778f0ee", "src": "hda", "uuid": "0b29bff0-7608-4968-bf7d-386788940dcb"}, "output_cn": {"id": "317a86e416b8a71d", "src": "hda", "uuid": "ea936c28-a559-41bd-a536-37be186894f0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of lines: total/processed: 184/184\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Number of lines: total/processed: 184/184\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": "2024-09-01 07:18:34", "plugin": "core", "name": "end_epoch", "raw_value": "1725175114.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 07:18:34", "plugin": "core", "name": "start_epoch", "raw_value": "1725175114.0000000"}, {"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_roh/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_roh", "tool_version": "1.10", "test_index": 0, "time_seconds": 12.391999959945679, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_roh/1.10-1", "has_data": true, "data": {"tool_id": "bcftools_roh", "tool_version": "1.10", "test_index": 1, "time_seconds": 33.19441509246826, "inputs": {"input_file": {"src": "hda", "id": "ead7bf0d85458c3d"}, "sec_general|AF_dflt": "0.4", "sec_general|GTs_only": "30", "output_type": "r"}, "job": {"model_class": "Job", "id": "581ba2a7c02bc8c2", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10", "state": "error", "exit_code": null, "create_time": "2024-09-01T07:19:24.218176", "update_time": "2024-09-01T07:19:35.013378", "galaxy_version": "24.1", "external_id": "gxy-7hsq2", "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/7/d/d/dataset_7ddd3cd7-be45-4a5a-919f-c925bdceb389.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools roh --AF-dflt \"0.4\" --GTs-only \"30.0\" --hw-to-az \"6.7e-08\" --az-to-hw \"5e-09\" --output-type r input.vcf.gz > '/galaxy/server/database/objects/b/0/9/dataset_b09e8e45-4aa5-4fea-8cff-63e68640ab3e.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"r\"", "sec_hmm": "{\"az_to_hw\": \"5e-09\", \"hw_to_az\": \"6.7e-08\", \"viterbi_training\": false}", "sec_general": "{\"AF_dflt\": \"0.4\", \"AF_file\": null, \"AF_tag\": \"\", \"GTs_only\": \"30.0\", \"buffer_overlap\": \"\", \"buffer_size\": \"\", \"estimate_AF\": null, \"genetic_map\": null, \"rec_rate\": \"\", \"sample\": null, \"skip_indels\": false}", "sec_restrict": "{\"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_file": {"id": "ead7bf0d85458c3d", "src": "hda", "uuid": "7ddd3cd7-be45-4a5a-919f-c925bdceb389"}}, "outputs": {"output_file": {"id": "8e3b6fdd7858e3d3", "src": "hda", "uuid": "b09e8e45-4aa5-4fea-8cff-63e68640ab3e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of target samples: 1\nNumber of --estimate-AF samples: 0\nNumber of sites in the buffer/overlap: unlimited\nNumber of lines total/processed: 8890/8888\nNumber of lines filtered/no AF/not biallelic/dup: 0/0/1/1\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "Number of target samples: 1\nNumber of --estimate-AF samples: 0\nNumber of sites in the buffer/overlap: unlimited\nNumber of lines total/processed: 8890/8888\nNumber of lines filtered/no AF/not biallelic/dup: 0/0/1/1\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, exit_code: None, stderr: Number of target samples: 1\nNumber of --estimate-AF samples: 0\nNumber of sites in the buffer/overlap: unlimited\nNumber of lines total/processed: 8890/8888\nNumber of lines filtered/no AF/not biallelic/dup: 0/0/1/1\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_roh/bcftools_roh/1.10, exit_code: None, stderr: Number of target samples: 1\nNumber of --estimate-AF samples: 0\nNumber of sites in the buffer/overlap: unlimited\nNumber of lines total/processed: 8890/8888\nNumber of lines filtered/no AF/not biallelic/dup: 0/0/1/1\n."], "status": "failure"}}, {"id": "deeptools_bam_coverage/3.3.2.0.0-0", "has_data": true, "data": {"tool_id": "deeptools_bam_coverage", "tool_version": "3.3.2.0.0", "test_index": 0, "time_seconds": 39.66051530838013, "inputs": {"bamInput": {"src": "hda", "id": "7bff4c686fa3fe0d"}, "binSize": "10", "scaling|type": "no", "outFileFormat": "bigwig", "advancedOpt|showAdvancedOpt": "no"}, "job": {"model_class": "Job", "id": "291a07c912f667a1", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:30:35.612528", "update_time": "2024-09-01T06:30:51.314037", "galaxy_version": "24.1", "external_id": "gxy-hlsz5", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/c/5/9/dataset_c595f591-f3ed-433b-b944-7752c93c45e9.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/0/b/9/metadata_0b9b2bf5-687e-4e41-b299-b1e547be5598.dat' one.bam.bai && bamCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bam one.bam --outFileName '/galaxy/server/database/objects/1/6/c/dataset_16c3a676-f899-4e6b-9656-271ee6be4799.dat' --outFileFormat 'bigwig' --binSize 10", "user_email": "tests@fake.org", "command_version": "bamCoverage 3.3.2", "params": {"binSize": "\"10\"", "scaling": "{\"__current_case__\": 3, \"type\": \"no\"}", "outFileFormat": "\"bigwig\"", "exactScaling": "false", "region": "\"\"", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"bam\""}, "inputs": {"bamInput": {"id": "7bff4c686fa3fe0d", "src": "hda", "uuid": "c595f591-f3ed-433b-b944-7752c93c45e9"}}, "outputs": {"outFileName": {"id": "291a07c912f667a1", "src": "hda", "uuid": "16c3a676-f899-4e6b-9656-271ee6be4799"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "bamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "bamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\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": "2024-09-01 06:30:38", "plugin": "core", "name": "end_epoch", "raw_value": "1725172238.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:30:37", "plugin": "core", "name": "start_epoch", "raw_value": "1725172237.0000000"}, {"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_bam_coverage/3.3.2.0.0-1", "has_data": true, "data": {"tool_id": "deeptools_bam_coverage", "tool_version": "3.3.2.0.0", "test_index": 1, "time_seconds": 39.43857431411743, "inputs": {"bamInput": {"src": "hda", "id": "747015e71ac9be6d"}, "binSize": "10", "scaling|effectiveGenomeSize|effectiveGenomeSize": "2451960000", "scaling|effectiveGenomeSize|effectiveGenomeSize_opt": "specific", "outFileFormat": "bigwig", "advancedOpt|showAdvancedOpt": "no"}, "job": {"model_class": "Job", "id": "039b04b47906a4fd", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:31:16.003999", "update_time": "2024-09-01T06:31:30.908461", "galaxy_version": "24.1", "external_id": "gxy-r29v4", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/9/b/5/dataset_9b512443-7bde-47c1-b49a-f9d138b8c1df.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/f/0/2/metadata_f02ecf28-9a29-4228-ace3-d15e07b258da.dat' one.bam.bai && bamCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bam one.bam --outFileName '/galaxy/server/database/objects/0/4/a/dataset_04a353fb-23f1-4d95-94fa-f7d38628609c.dat' --outFileFormat 'bigwig' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000", "user_email": "tests@fake.org", "command_version": "bamCoverage 3.3.2", "params": {"binSize": "\"10\"", "scaling": "{\"__current_case__\": 4, \"effectiveGenomeSize\": {\"__current_case__\": 0, \"effectiveGenomeSize\": \"2451960000\", \"effectiveGenomeSize_opt\": \"specific\"}, \"type\": \"1x\"}", "outFileFormat": "\"bigwig\"", "exactScaling": "false", "region": "\"\"", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"bam\""}, "inputs": {"bamInput": {"id": "747015e71ac9be6d", "src": "hda", "uuid": "9b512443-7bde-47c1-b49a-f9d138b8c1df"}}, "outputs": {"outFileName": {"id": "039b04b47906a4fd", "src": "hda", "uuid": "04a353fb-23f1-4d95-94fa-f7d38628609c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:31:17", "plugin": "core", "name": "start_epoch", "raw_value": "1725172277.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:31:18", "plugin": "core", "name": "end_epoch", "raw_value": "1725172278.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "deeptools_bam_coverage/3.3.2.0.0-2", "has_data": true, "data": {"tool_id": "deeptools_bam_coverage", "tool_version": "3.3.2.0.0", "test_index": 2, "time_seconds": 40.35533380508423, "inputs": {"bamInput": {"src": "hda", "id": "62eb354288db9131"}, "binSize": "10", "scaling|effectiveGenomeSize|effectiveGenomeSize": "2451960000", "scaling|effectiveGenomeSize|effectiveGenomeSize_opt": "specific", "outFileFormat": "bedgraph", "advancedOpt|showAdvancedOpt": "no"}, "job": {"model_class": "Job", "id": "db7aa3e9d708521c", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:31:55.435061", "update_time": "2024-09-01T06:32:11.292553", "galaxy_version": "24.1", "external_id": "gxy-c6knr", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/8/1/0/dataset_8106cd4c-e081-41d5-803f-b495062089a2.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/4/f/a/metadata_4fafdf85-c6e3-4489-bd74-4823e79dbea0.dat' one.bam.bai && bamCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bam one.bam --outFileName '/galaxy/server/database/objects/9/2/1/dataset_92191f1b-1b0c-4954-8eb1-15b1a62c3779.dat' --outFileFormat 'bedgraph' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000", "user_email": "tests@fake.org", "command_version": "bamCoverage 3.3.2", "params": {"binSize": "\"10\"", "scaling": "{\"__current_case__\": 4, \"effectiveGenomeSize\": {\"__current_case__\": 0, \"effectiveGenomeSize\": \"2451960000\", \"effectiveGenomeSize_opt\": \"specific\"}, \"type\": \"1x\"}", "outFileFormat": "\"bedgraph\"", "exactScaling": "false", "region": "\"\"", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"bam\""}, "inputs": {"bamInput": {"id": "62eb354288db9131", "src": "hda", "uuid": "8106cd4c-e081-41d5-803f-b495062089a2"}}, "outputs": {"outFileName": {"id": "db7aa3e9d708521c", "src": "hda", "uuid": "92191f1b-1b0c-4954-8eb1-15b1a62c3779"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:31:58", "plugin": "core", "name": "start_epoch", "raw_value": "1725172318.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:31:58", "plugin": "core", "name": "end_epoch", "raw_value": "1725172318.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}]}, "status": "success"}}, {"id": "deeptools_bam_coverage/3.3.2.0.0-3", "has_data": true, "data": {"tool_id": "deeptools_bam_coverage", "tool_version": "3.3.2.0.0", "test_index": 3, "time_seconds": 39.44861841201782, "inputs": {"bamInput": {"src": "hda", "id": "d407cd50fc80b371"}, "binSize": "10", "scaling|effectiveGenomeSize|effectiveGenomeSize": "2451960000", "scaling|effectiveGenomeSize|effectiveGenomeSize_opt": "specific", "outFileFormat": "bigwig", "advancedOpt|showAdvancedOpt": "no"}, "job": {"model_class": "Job", "id": "6b86f185bc26f926", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:32:34.971291", "update_time": "2024-09-01T06:32:50.732849", "galaxy_version": "24.1", "external_id": "gxy-nnwgh", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/3/f/7/dataset_3f76ef28-3462-4bc1-98e1-0985e3efdb39.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/9/5/0/metadata_950f8f7c-b220-4618-9644-40fb57662cd5.dat' one.bam.bai && bamCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bam one.bam --outFileName '/galaxy/server/database/objects/f/1/f/dataset_f1fcdd57-c3b1-4c2a-aba3-0ca7ebee4435.dat' --outFileFormat 'bigwig' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000", "user_email": "tests@fake.org", "command_version": "bamCoverage 3.3.2", "params": {"binSize": "\"10\"", "scaling": "{\"__current_case__\": 4, \"effectiveGenomeSize\": {\"__current_case__\": 0, \"effectiveGenomeSize\": \"2451960000\", \"effectiveGenomeSize_opt\": \"specific\"}, \"type\": \"1x\"}", "outFileFormat": "\"bigwig\"", "exactScaling": "false", "region": "\"\"", "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"bam\""}, "inputs": {"bamInput": {"id": "d407cd50fc80b371", "src": "hda", "uuid": "3f76ef28-3462-4bc1-98e1-0985e3efdb39"}}, "outputs": {"outFileName": {"id": "6b86f185bc26f926", "src": "hda", "uuid": "f1fcdd57-c3b1-4c2a-aba3-0ca7ebee4435"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:32:36", "plugin": "core", "name": "start_epoch", "raw_value": "1725172356.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:32:37", "plugin": "core", "name": "end_epoch", "raw_value": "1725172357.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "deeptools_bam_coverage/3.3.2.0.0-4", "has_data": true, "data": {"tool_id": "deeptools_bam_coverage", "tool_version": "3.3.2.0.0", "test_index": 4, "time_seconds": 40.115328311920166, "inputs": {"bamInput": {"src": "hda", "id": "ee80714db48dd321"}, "binSize": "10", "scaling|effectiveGenomeSize|effectiveGenomeSize": "2451960000", "scaling|effectiveGenomeSize|effectiveGenomeSize_opt": "specific", "outFileFormat": "bedgraph", "advancedOpt|showAdvancedOpt": "yes"}, "job": {"model_class": "Job", "id": "c3ae4a450c53f67c", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:33:15.150781", "update_time": "2024-09-01T06:33:31.049837", "galaxy_version": "24.1", "external_id": "gxy-zl6zv", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/0/a/1/dataset_0a1d6f8b-c4d8-4c6d-a0b5-b6157c1bc6d5.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/d/3/d/metadata_d3d97025-a6bd-4d03-b3c3-301d169c5c22.dat' one.bam.bai && bamCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bam one.bam --outFileName '/galaxy/server/database/objects/4/2/5/dataset_42531be2-fe52-405c-9cf4-f13a2104aef4.dat' --outFileFormat 'bedgraph' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000 --scaleFactor 1.0 --minMappingQuality '1'", "user_email": "tests@fake.org", "command_version": "bamCoverage 3.3.2", "params": {"binSize": "\"10\"", "scaling": "{\"__current_case__\": 4, \"effectiveGenomeSize\": {\"__current_case__\": 0, \"effectiveGenomeSize\": \"2451960000\", \"effectiveGenomeSize_opt\": \"specific\"}, \"type\": \"1x\"}", "outFileFormat": "\"bedgraph\"", "exactScaling": "false", "region": "\"\"", "advancedOpt": "{\"MNase\": false, \"Offset\": \"\", \"__current_case__\": 1, \"blackListFileName\": null, \"centerReads\": false, \"doExtendCustom\": {\"__current_case__\": 0, \"doExtend\": \"no\"}, \"filterRNAstrand\": \"no\", \"ignoreDuplicates\": false, \"ignoreForNormalization\": \"\", \"maxFragmentLength\": \"0\", \"minFragmentLength\": \"0\", \"minMappingQuality\": \"1\", \"samFlagExclude\": \"\", \"samFlagInclude\": \"\", \"scaleFactor\": \"1.0\", \"showAdvancedOpt\": \"yes\", \"skipNAs\": false, \"smoothLength\": \"\"}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"bam\""}, "inputs": {"bamInput": {"id": "ee80714db48dd321", "src": "hda", "uuid": "0a1d6f8b-c4d8-4c6d-a0b5-b6157c1bc6d5"}}, "outputs": {"outFileName": {"id": "c3ae4a450c53f67c", "src": "hda", "uuid": "42531be2-fe52-405c-9cf4-f13a2104aef4"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: 1\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: 1\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:33:16", "plugin": "core", "name": "start_epoch", "raw_value": "1725172396.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:33:17", "plugin": "core", "name": "end_epoch", "raw_value": "1725172397.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "deeptools_bam_coverage/3.3.2.0.0-5", "has_data": true, "data": {"tool_id": "deeptools_bam_coverage", "tool_version": "3.3.2.0.0", "test_index": 5, "time_seconds": 39.3248188495636, "inputs": {"bamInput": {"src": "hda", "id": "4f5d07211d88a9c1"}, "binSize": "10", "scaling|effectiveGenomeSize|effectiveGenomeSize": "2451960000", "scaling|effectiveGenomeSize|effectiveGenomeSize_opt": "specific", "outFileFormat": "bigwig", "advancedOpt|filterRNAstrand": "reverse", "advancedOpt|showAdvancedOpt": "yes"}, "job": {"model_class": "Job", "id": "79118445a2ae4924", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:33:54.526412", "update_time": "2024-09-01T06:34:10.426681", "galaxy_version": "24.1", "external_id": "gxy-tmb9t", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/c/6/6/dataset_c6600866-0b22-4ff2-826b-6f098e3bc49f.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/3/6/0/metadata_3604f9d6-23bb-4ac7-b626-3516837054ee.dat' one.bam.bai && bamCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bam one.bam --outFileName '/galaxy/server/database/objects/a/5/9/dataset_a596fcdc-c114-4673-9d57-ce7c76c8707e.dat' --outFileFormat 'bigwig' --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2451960000 --scaleFactor 1.0 --minMappingQuality '1' --filterRNAstrand 'reverse'", "user_email": "tests@fake.org", "command_version": "bamCoverage 3.3.2", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"MNase\": false, \"Offset\": \"\", \"__current_case__\": 1, \"blackListFileName\": null, \"centerReads\": false, \"doExtendCustom\": {\"__current_case__\": 0, \"doExtend\": \"no\"}, \"filterRNAstrand\": \"reverse\", \"ignoreDuplicates\": false, \"ignoreForNormalization\": \"\", \"maxFragmentLength\": \"0\", \"minFragmentLength\": \"0\", \"minMappingQuality\": \"1\", \"samFlagExclude\": \"\", \"samFlagInclude\": \"\", \"scaleFactor\": \"1.0\", \"showAdvancedOpt\": \"yes\", \"skipNAs\": false, \"smoothLength\": \"\"}", "region": "\"\"", "exactScaling": "false", "outFileFormat": "\"bigwig\"", "scaling": "{\"__current_case__\": 4, \"effectiveGenomeSize\": {\"__current_case__\": 0, \"effectiveGenomeSize\": \"2451960000\", \"effectiveGenomeSize_opt\": \"specific\"}, \"type\": \"1x\"}", "binSize": "\"10\""}, "inputs": {"bamInput": {"id": "4f5d07211d88a9c1", "src": "hda", "uuid": "c6600866-0b22-4ff2-826b-6f098e3bc49f"}}, "outputs": {"outFileName": {"id": "79118445a2ae4924", "src": "hda", "uuid": "a596fcdc-c114-4673-9d57-ce7c76c8707e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Due to filtering, 51.08108108108108% of the aforementioned alignments will be used 1115.6108108108108\n", "tool_stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: 1\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\nfilter_strand: reverse\nOffset: [1, -1]\n", "job_stdout": "", "job_stderr": "", "stdout": "Due to filtering, 51.08108108108108% of the aforementioned alignments will be used 1115.6108108108108\n", "stderr": "normalization: 1x (effective genome size 2451960000)\nbamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: 1\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\nfilter_strand: reverse\nOffset: [1, -1]\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:33:56", "plugin": "core", "name": "start_epoch", "raw_value": "1725172436.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:33:57", "plugin": "core", "name": "end_epoch", "raw_value": "1725172437.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "deeptools_bam_coverage/3.3.2.0.0-6", "has_data": true, "data": {"tool_id": "deeptools_bam_coverage", "tool_version": "3.3.2.0.0", "test_index": 6, "time_seconds": 39.33525109291077, "inputs": {"bamInput": {"src": "hda", "id": "e504eb56c1c09b43"}, "binSize": "10", "scaling|type": "no", "outFileFormat": "bigwig", "advancedOpt|doExtendCustom|doExtend": "yes", "advancedOpt|minMappingQuality": "0", "advancedOpt|Offset": "-4 -1", "advancedOpt|showAdvancedOpt": "yes"}, "job": {"model_class": "Job", "id": "b79312f9873019a0", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:34:33.954591", "update_time": "2024-09-01T06:34:49.685877", "galaxy_version": "24.1", "external_id": "gxy-5b8cs", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/f/4/c/dataset_f4cd15b5-d1f8-4d0b-8c8f-5f8e067256ae.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/d/4/b/metadata_d4b14fcc-d2b7-466d-a8d2-dc059e99d956.dat' one.bam.bai && bamCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bam one.bam --outFileName '/galaxy/server/database/objects/0/7/6/dataset_07683aba-b4ae-4273-a61f-cceb5a59900c.dat' --outFileFormat 'bigwig' --binSize 10 --scaleFactor 1.0 --extendReads --Offset -4 -1", "user_email": "tests@fake.org", "command_version": "bamCoverage 3.3.2", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"MNase\": false, \"Offset\": \"-4 -1\", \"__current_case__\": 1, \"blackListFileName\": null, \"centerReads\": false, \"doExtendCustom\": {\"__current_case__\": 1, \"doExtend\": \"yes\"}, \"filterRNAstrand\": \"no\", \"ignoreDuplicates\": false, \"ignoreForNormalization\": \"\", \"maxFragmentLength\": \"0\", \"minFragmentLength\": \"0\", \"minMappingQuality\": \"0\", \"samFlagExclude\": \"\", \"samFlagInclude\": \"\", \"scaleFactor\": \"1.0\", \"showAdvancedOpt\": \"yes\", \"skipNAs\": false, \"smoothLength\": \"\"}", "region": "\"\"", "exactScaling": "false", "outFileFormat": "\"bigwig\"", "scaling": "{\"__current_case__\": 3, \"type\": \"no\"}", "binSize": "\"10\""}, "inputs": {"bamInput": {"id": "e504eb56c1c09b43", "src": "hda", "uuid": "f4cd15b5-d1f8-4d0b-8c8f-5f8e067256ae"}}, "outputs": {"outFileName": {"id": "b79312f9873019a0", "src": "hda", "uuid": "07683aba-b4ae-4273-a61f-cceb5a59900c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "bamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: 242\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 968\nfilter_strand: None\nOffset: [-4, -1]\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "bamFilesList: ['one.bam']\nbinLength: 10\nnumberOfSamples: None\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: 242\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 10\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 968\nfilter_strand: None\nOffset: [-4, -1]\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:34:35", "plugin": "core", "name": "start_epoch", "raw_value": "1725172475.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:34:36", "plugin": "core", "name": "end_epoch", "raw_value": "1725172476.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "deeptools_compute_matrix/3.3.2.0.0-0", "has_data": true, "data": {"tool_id": "deeptools_compute_matrix", "tool_version": "3.3.2.0.0", "test_index": 0, "time_seconds": 117.45303177833557, "inputs": {"regionsFiles_0|regionsFile": {"src": "hda", "id": "0f5f5d39c9be041a"}, "multibigwig_conditional|bigwigfiles": {"src": "hda", "id": "71d0106886a7baee"}, "mode|beforeRegionStartLength": "10", "mode|afterRegionStartLength": "10", "mode|mode_select": "reference-point", "advancedOpt|binSize": "10", "advancedOpt|sortUsing": "sum", "advancedOpt|averageTypeBins": "sum", "advancedOpt|showAdvancedOpt": "yes"}, "job": {"model_class": "Job", "id": "19bc0e5055a63b46", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:27:44.873358", "update_time": "2024-09-01T06:28:50.538349", "galaxy_version": "24.1", "external_id": "gxy-v4nmp", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/5/f/d/dataset_5fd2a92b-779d-4985-b549-addcc5ecc452.dat' 'bamCoverage_result4.bw_0.bw' && ln -f -s '/galaxy/server/database/objects/9/a/5/dataset_9a53b94e-a94d-4433-b0b6-895fcfe0230e.dat' 'computeMatrix1_bed_0.bed' && computeMatrix reference-point --regionsFileName 'computeMatrix1_bed_0.bed' --scoreFileName 'bamCoverage_result4.bw_0.bw' --outFileName '/galaxy/server/database/objects/9/0/8/dataset_908520e4-0193-468b-a944-c2507340e60e.dat' --samplesLabel 'bamCoverage_result4.bw' --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --referencePoint TSS --beforeRegionStartLength 10 --afterRegionStartLength 10 --sortRegions 'keep' --sortUsing 'sum' --averageTypeBins 'sum' --binSize 10 --transcriptID transcript --exonID exon --transcript_id_designator transcript_id", "user_email": "tests@fake.org", "command_version": "computeMatrix 3.3.2", "params": {"__input_ext": "\"bed\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 1, \"averageTypeBins\": \"sum\", \"binSize\": \"10\", \"blackListFileName\": null, \"exonID\": \"exon\", \"maxThreshold\": \"\", \"metagene\": false, \"minThreshold\": \"\", \"missingDataAsZero\": false, \"scale\": \"\", \"showAdvancedOpt\": \"yes\", \"skipZeros\": false, \"sortRegions\": \"keep\", \"sortUsing\": \"sum\", \"transcriptID\": \"transcript\", \"transcript_id_designator\": \"transcript_id\"}", "output": "{\"__current_case__\": 0, \"showOutputSettings\": \"no\"}", "mode": "{\"__current_case__\": 1, \"afterRegionStartLength\": \"10\", \"beforeRegionStartLength\": \"10\", \"mode_select\": \"reference-point\", \"nanAfterEnd\": false, \"referencePoint\": \"TSS\"}", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibigwig_conditional": "{\"__current_case__\": 0, \"bigwigfiles\": {\"values\": [{\"id\": 2, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}", "regionsFiles": "[{\"__index__\": 0, \"regionsFile\": {\"values\": [{\"id\": 1, \"src\": \"hda\"}]}}]"}, "inputs": {"multibigwig_conditional|bigwigfiles1": {"id": "71d0106886a7baee", "src": "hda", "uuid": "5fd2a92b-779d-4985-b549-addcc5ecc452"}, "multibigwig_conditional|bigwigfiles": {"id": "71d0106886a7baee", "src": "hda", "uuid": "5fd2a92b-779d-4985-b549-addcc5ecc452"}, "regionsFiles_0|regionsFile": {"id": "0f5f5d39c9be041a", "src": "hda", "uuid": "9a53b94e-a94d-4433-b0b6-895fcfe0230e"}}, "outputs": {"outFileName": {"id": "19bc0e5055a63b46", "src": "hda", "uuid": "908520e4-0193-468b-a944-c2507340e60e"}}, "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": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:28:31", "plugin": "core", "name": "end_epoch", "raw_value": "1725172111.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:28:29", "plugin": "core", "name": "start_epoch", "raw_value": "1725172109.0000000"}, {"title": "Memory Allocated (MB)", "value": "32212", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32212.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "deeptools_compute_matrix/3.3.2.0.0-1", "has_data": true, "data": {"tool_id": "deeptools_compute_matrix", "tool_version": "3.3.2.0.0", "test_index": 1, "time_seconds": 40.09795951843262, "inputs": {"regionsFiles_0|regionsFile": {"src": "hda", "id": "a6c3c1dd0dbc7064"}, "multibigwig_conditional|bigwigfiles": {"src": "hda", "id": "f4e8f03b50f50385"}, "mode|beforeRegionStartLength": "10", "mode|afterRegionStartLength": "10", "mode|mode_select": "reference-point", "advancedOpt|binSize": "10", "advancedOpt|showAdvancedOpt": "yes"}, "job": {"model_class": "Job", "id": "b7124d2765df34d0", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:29:13.781803", "update_time": "2024-09-01T06:29:30.462932", "galaxy_version": "24.1", "external_id": "gxy-v6v8q", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/d/4/e/dataset_d4e8e7f7-b21b-4b1c-8020-59c71bee9810.dat' 'computeMatrix2.bw_0.bw' && ln -f -s '/galaxy/server/database/objects/0/3/a/dataset_03ac7313-1195-4c13-8f6c-b3ccf515c843.dat' 'computeMatrix2_bed_0.bed' && computeMatrix reference-point --regionsFileName 'computeMatrix2_bed_0.bed' --scoreFileName 'computeMatrix2.bw_0.bw' --outFileName '/galaxy/server/database/objects/7/6/3/dataset_76365fac-8237-4442-a9be-2d03af43fd37.dat' --samplesLabel 'computeMatrix2.bw' --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --referencePoint TSS --beforeRegionStartLength 10 --afterRegionStartLength 10 --sortRegions 'keep' --sortUsing 'mean' --averageTypeBins 'mean' --binSize 10 --transcriptID transcript --exonID exon --transcript_id_designator transcript_id", "user_email": "tests@fake.org", "command_version": "computeMatrix 3.3.2", "params": {"__input_ext": "\"bed\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 1, \"averageTypeBins\": \"mean\", \"binSize\": \"10\", \"blackListFileName\": null, \"exonID\": \"exon\", \"maxThreshold\": \"\", \"metagene\": false, \"minThreshold\": \"\", \"missingDataAsZero\": false, \"scale\": \"\", \"showAdvancedOpt\": \"yes\", \"skipZeros\": false, \"sortRegions\": \"keep\", \"sortUsing\": \"mean\", \"transcriptID\": \"transcript\", \"transcript_id_designator\": \"transcript_id\"}", "output": "{\"__current_case__\": 0, \"showOutputSettings\": \"no\"}", "mode": "{\"__current_case__\": 1, \"afterRegionStartLength\": \"10\", \"beforeRegionStartLength\": \"10\", \"mode_select\": \"reference-point\", \"nanAfterEnd\": false, \"referencePoint\": \"TSS\"}", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibigwig_conditional": "{\"__current_case__\": 0, \"bigwigfiles\": {\"values\": [{\"id\": 5, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}", "regionsFiles": "[{\"__index__\": 0, \"regionsFile\": {\"values\": [{\"id\": 4, \"src\": \"hda\"}]}}]"}, "inputs": {"multibigwig_conditional|bigwigfiles1": {"id": "f4e8f03b50f50385", "src": "hda", "uuid": "d4e8e7f7-b21b-4b1c-8020-59c71bee9810"}, "multibigwig_conditional|bigwigfiles": {"id": "f4e8f03b50f50385", "src": "hda", "uuid": "d4e8e7f7-b21b-4b1c-8020-59c71bee9810"}, "regionsFiles_0|regionsFile": {"id": "a6c3c1dd0dbc7064", "src": "hda", "uuid": "03ac7313-1195-4c13-8f6c-b3ccf515c843"}}, "outputs": {"outFileName": {"id": "b7124d2765df34d0", "src": "hda", "uuid": "76365fac-8237-4442-a9be-2d03af43fd37"}}, "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": "2024-09-01 06:29:16", "plugin": "core", "name": "end_epoch", "raw_value": "1725172156.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:29:15", "plugin": 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0, "create_time": "2024-09-01T06:29:54.646224", "update_time": "2024-09-01T06:30:10.893688", "galaxy_version": "24.1", "external_id": "gxy-4knjr", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/2/7/9/dataset_27994a01-e544-43d8-be58-bde7eaeaa257.dat' 'computeMatrix2.bw_0.bw' && ln -f -s '/galaxy/server/database/objects/2/4/f/dataset_24f68c12-e66b-4a35-bd7b-21e6ab41da93.dat' 'computeMatrix2_bed_0.bed' && computeMatrix scale-regions --regionsFileName 'computeMatrix2_bed_0.bed' --scoreFileName 'computeMatrix2.bw_0.bw' --outFileName '/galaxy/server/database/objects/2/6/a/dataset_26acfa3a-91eb-42f6-8220-00aba6b0ae85.dat' --samplesLabel 'computeMatrix2.bw' --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --regionBodyLength 500 --sortRegions 'keep' --sortUsing 'mean' --averageTypeBins 'mean' --binSize 50 --transcriptID transcript --exonID exon --transcript_id_designator transcript_id", "user_email": "tests@fake.org", "command_version": "computeMatrix 3.3.2", "params": {"__input_ext": "\"bed\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advancedOpt": "{\"__current_case__\": 1, \"averageTypeBins\": \"mean\", \"binSize\": \"50\", \"blackListFileName\": null, \"exonID\": \"exon\", \"maxThreshold\": \"\", \"metagene\": false, \"minThreshold\": \"\", \"missingDataAsZero\": false, \"scale\": \"\", \"showAdvancedOpt\": \"yes\", \"skipZeros\": false, \"sortRegions\": \"keep\", \"sortUsing\": \"mean\", \"transcriptID\": \"transcript\", \"transcript_id_designator\": \"transcript_id\"}", "output": "{\"__current_case__\": 0, \"showOutputSettings\": \"no\"}", "mode": "{\"__current_case__\": 0, \"mode_select\": \"scale-regions\", \"regionBodyLength\": \"500\", \"regionStartLength\": {\"__current_case__\": 0, \"regionStartLength_select\": \"no\"}}", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibigwig_conditional": "{\"__current_case__\": 0, \"bigwigfiles\": {\"values\": [{\"id\": 8, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}", "regionsFiles": "[{\"__index__\": 0, \"regionsFile\": {\"values\": [{\"id\": 7, \"src\": \"hda\"}]}}]"}, "inputs": {"multibigwig_conditional|bigwigfiles1": {"id": "ac9b4d9a06230776", "src": "hda", "uuid": "27994a01-e544-43d8-be58-bde7eaeaa257"}, "multibigwig_conditional|bigwigfiles": {"id": "ac9b4d9a06230776", "src": "hda", "uuid": "27994a01-e544-43d8-be58-bde7eaeaa257"}, "regionsFiles_0|regionsFile": {"id": "65c15b69694655c0", "src": "hda", "uuid": "24f68c12-e66b-4a35-bd7b-21e6ab41da93"}}, "outputs": {"outFileName": {"id": "0b8dda5741c86c37", "src": "hda", "uuid": "26acfa3a-91eb-42f6-8220-00aba6b0ae85"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "A region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) ca5 ch2:125:150. Skipping...\nA region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) cda5 ch2:150:175. Skipping...\nA region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) ca8 ch3:75:100. Skipping...\nA region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) cda8 ch3:100:125. Skipping...\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "A region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) ca5 ch2:125:150. Skipping...\nA region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) cda5 ch2:150:175. Skipping...\nA region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) ca8 ch3:75:100. Skipping...\nA region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (25) cda8 ch3:100:125. Skipping...\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:29:58", "plugin": "core", "name": "end_epoch", "raw_value": "1725172198.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:29:56", "plugin": "core", "name": "start_epoch", "raw_value": "1725172196.0000000"}, {"title": "Memory Allocated (MB)", "value": "32212", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32212.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "freebayes/1.3.6+galaxy0-0", "has_data": true, "data": {"tool_id": "freebayes", "tool_version": "1.3.6+galaxy0", "test_index": 0, "time_seconds": 48.01842641830444, "inputs": {"reference_source|batchmode|input_bams": {"src": "hda", "id": "2e1ca6840072df82"}, "reference_source|batchmode|processmode": "individual", "reference_source|ref_file": {"src": "hda", "id": "30ab78c12e6da60d"}, "reference_source|reference_source_selector": "history", "options_type|options_type_selector": "simple"}, "job": {"model_class": "Job", "id": "3ccef5de04c0d2f2", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T07:11:25.212431", "update_time": "2024-09-01T07:11:48.753538", "galaxy_version": "24.1", "external_id": "gxy-brr75", "handler": null, "job_runner_name": null, "command_line": "ln -s -f '/galaxy/server/database/objects/5/d/0/dataset_5d0342e0-a336-41c1-847f-f8929614d1c3.dat' 'localref.fa' && samtools faidx 'localref.fa' 2>&1 || echo \"Error running samtools faidx for FreeBayes\" >&2 && ln -s -f '/galaxy/server/database/objects/2/5/b/dataset_25bc5af5-9e4a-4915-8091-efa212eae527.dat' 'b_0.bam' && ln -s -f '/galaxy/server/database/objects/_metadata_files/1/6/3/metadata_1635ef16-4d0c-49c5-af34-acea080f6598.dat' 'b_0.bam.bai' && samtools view -H b_0.bam| grep '^@SQ' | cut -f 2- | awk '{ gsub(\"^SN:\",\"\",$1); gsub(\"^LN:\",\"\",$2); print $1\"\\t0\\t\"$2; }' >> regions_all.bed && sort -u regions_all.bed > regions_uniq.bed && mkdir vcf_output failed_alleles trace && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do echo \" freebayes --region '$i' --bam 'b_0.bam' --fasta-reference 'localref.fa' --vcf './vcf_output/part_$i.vcf' \"; done > freebayes_commands.sh && cat freebayes_commands.sh | parallel --will-cite -j ${GALAXY_SLOTS:-1} && grep \"^#\" \"./vcf_output/part_$i.vcf\" > header.txt && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do cat \"./vcf_output/part_$i.vcf\" | grep -v \"^#\" || true ; done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '/galaxy/server/database/objects/0/e/6/dataset_0e62c8f9-0289-4df5-9520-d0a235050f28.dat'", "user_email": "tests@fake.org", "command_version": "1.3.6", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"options_type_selector\": \"simple\"}", "coverage_options": "{\"__current_case__\": 1, \"coverage_options_selector\": \"do_not_set\"}", "target_limit_type": "{\"__current_case__\": 0, \"target_limit_type_selector\": \"do_not_limit\"}", "reference_source": "{\"__current_case__\": 1, \"batchmode\": {\"__current_case__\": 0, \"input_bams\": {\"values\": [{\"id\": 342, \"src\": \"hda\"}]}, \"processmode\": \"individual\"}, \"ref_file\": {\"values\": [{\"id\": 343, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|batchmode|input_bams": {"id": "2e1ca6840072df82", "src": "hda", "uuid": "25bc5af5-9e4a-4915-8091-efa212eae527"}, "reference_source|ref_file": {"id": "30ab78c12e6da60d", "src": "hda", "uuid": "5d0342e0-a336-41c1-847f-f8929614d1c3"}}, "outputs": {"output_vcf": {"id": "7eb055c8813154e4", "src": "hda", "uuid": "0e62c8f9-0289-4df5-9520-d0a235050f28"}}, "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": "2024-09-01 07:11:33", "plugin": "core", "name": "end_epoch", "raw_value": "1725174693.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 07:11:32", "plugin": "core", "name": "start_epoch", "raw_value": "1725174692.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "freebayes/1.3.6+galaxy0-1", "has_data": true, "data": {"tool_id": "freebayes", "tool_version": "1.3.6+galaxy0", "test_index": 1, "time_seconds": 29.972146034240723, "inputs": {"reference_source|batchmode|input_bams": {"src": "hda", "id": "cd7534d53f3302d3"}, "reference_source|batchmode|processmode": "individual", "reference_source|ref_file": {"src": "hda", "id": "77e464c82d2dd442"}, "reference_source|reference_source_selector": "history", "coverage_options|min_coverage": "14", "coverage_options|coverage_options_selector": "set", "options_type|options_type_selector": "naive_w_filters"}, "job": {"model_class": "Job", "id": "28e6fe619e9e1c2d", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0", "state": "error", "exit_code": null, "create_time": "2024-09-01T07:12:12.934841", "update_time": "2024-09-01T07:12:18.837353", "galaxy_version": "24.1", "external_id": "gxy-57kmf", "handler": null, "job_runner_name": null, "command_line": "ln -s -f '/galaxy/server/database/objects/5/4/0/dataset_54058f86-0e55-4242-8e7c-69e29d989e47.dat' 'localref.fa' && samtools faidx 'localref.fa' 2>&1 || echo \"Error running samtools faidx for FreeBayes\" >&2 && ln -s -f '/galaxy/server/database/objects/9/1/9/dataset_9196fc04-b291-4934-9ca7-95edcbf7aa6d.dat' 'b_0.bam' && ln -s -f '/galaxy/server/database/objects/_metadata_files/0/8/c/metadata_08ceb78f-5a73-48fa-a0a1-d6361e1ca94b.dat' 'b_0.bam.bai' && samtools view -H b_0.bam| grep '^@SQ' | cut -f 2- | awk '{ gsub(\"^SN:\",\"\",$1); gsub(\"^LN:\",\"\",$2); print $1\"\\t0\\t\"$2; }' >> regions_all.bed && sort -u regions_all.bed > regions_uniq.bed && mkdir vcf_output failed_alleles trace && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do echo \" freebayes --region '$i' --bam 'b_0.bam' --fasta-reference 'localref.fa' --vcf './vcf_output/part_$i.vcf' --min-coverage 14 --skip-coverage 0 --limit-coverage 0 --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0.05 --pooled-continuous --report-monomorphic --standard-filters \"; done > freebayes_commands.sh && cat freebayes_commands.sh | parallel --will-cite -j ${GALAXY_SLOTS:-1} && grep \"^#\" \"./vcf_output/part_$i.vcf\" > header.txt && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do cat \"./vcf_output/part_$i.vcf\" | grep -v \"^#\" || true ; done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '/galaxy/server/database/objects/1/3/1/dataset_13188573-d0df-4046-b4a6-2da6796dbc9f.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 4, \"options_type_selector\": \"naive_w_filters\"}", "coverage_options": "{\"__current_case__\": 0, \"coverage_options_selector\": \"set\", \"limit_coverage\": \"0\", \"min_coverage\": \"14\", \"skip_coverage\": \"0\"}", "target_limit_type": "{\"__current_case__\": 0, \"target_limit_type_selector\": \"do_not_limit\"}", "reference_source": "{\"__current_case__\": 1, \"batchmode\": {\"__current_case__\": 0, \"input_bams\": {\"values\": [{\"id\": 345, \"src\": \"hda\"}]}, \"processmode\": \"individual\"}, \"ref_file\": {\"values\": [{\"id\": 346, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|batchmode|input_bams": {"id": "cd7534d53f3302d3", "src": "hda", "uuid": "9196fc04-b291-4934-9ca7-95edcbf7aa6d"}, "reference_source|ref_file": {"id": "77e464c82d2dd442", "src": "hda", "uuid": "54058f86-0e55-4242-8e7c-69e29d989e47"}}, "outputs": {"output_vcf": {"id": "0d42b19d3e5ce231", "src": "hda", "uuid": "13188573-d0df-4046-b4a6-2da6796dbc9f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "freebayes/1.3.6+galaxy0-2", "has_data": true, "data": {"tool_id": "freebayes", "tool_version": "1.3.6+galaxy0", "test_index": 2, "time_seconds": 40.99004864692688, "inputs": {"reference_source|batchmode|input_bams": {"src": "hda", "id": "a7a65e481b711ac7"}, "reference_source|batchmode|processmode": "individual", "reference_source|ref_file": {"src": "hda", "id": "27180e95bcf1e9cc"}, "reference_source|reference_source_selector": "history", "coverage_options|min_coverage": "14", "coverage_options|coverage_options_selector": "set", "options_type|options_type_selector": "naive_w_filters"}, "job": {"model_class": "Job", "id": "77bb97717ea8b08c", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T07:12:43.642731", "update_time": "2024-09-01T07:12:59.772999", "galaxy_version": "24.1", "external_id": "gxy-tg5qt", "handler": null, "job_runner_name": null, "command_line": "ln -s -f '/galaxy/server/database/objects/c/c/2/dataset_cc2de2f2-86d9-4af0-9a93-2c08e4bfc2e7.dat' 'localref.fa' && samtools faidx 'localref.fa' 2>&1 || echo \"Error running samtools faidx for FreeBayes\" >&2 && ln -s -f '/galaxy/server/database/objects/6/8/f/dataset_68fce152-e077-461b-882f-4cee31ebedcd.dat' 'b_0.bam' && ln -s -f '/galaxy/server/database/objects/_metadata_files/b/2/e/metadata_b2eab9c8-9976-407c-b11f-4907ccb97674.dat' 'b_0.bam.bai' && samtools view -H b_0.bam| grep '^@SQ' | cut -f 2- | awk '{ gsub(\"^SN:\",\"\",$1); gsub(\"^LN:\",\"\",$2); print $1\"\\t0\\t\"$2; }' >> regions_all.bed && sort -u regions_all.bed > regions_uniq.bed && mkdir vcf_output failed_alleles trace && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do echo \" freebayes --region '$i' --bam 'b_0.bam' --fasta-reference 'localref.fa' --vcf './vcf_output/part_$i.vcf' --min-coverage 14 --skip-coverage 0 --limit-coverage 0 --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0.05 --pooled-continuous --report-monomorphic --standard-filters \"; done > freebayes_commands.sh && cat freebayes_commands.sh | parallel --will-cite -j ${GALAXY_SLOTS:-1} && grep \"^#\" \"./vcf_output/part_$i.vcf\" > header.txt && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do cat \"./vcf_output/part_$i.vcf\" | grep -v \"^#\" || true ; done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '/galaxy/server/database/objects/d/5/d/dataset_d5ddc6fd-2d39-4560-8446-f0e7070e221b.dat'", "user_email": "tests@fake.org", "command_version": "1.3.6", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 4, \"options_type_selector\": \"naive_w_filters\"}", "coverage_options": "{\"__current_case__\": 0, \"coverage_options_selector\": \"set\", \"limit_coverage\": \"0\", \"min_coverage\": \"14\", \"skip_coverage\": \"0\"}", "target_limit_type": "{\"__current_case__\": 0, \"target_limit_type_selector\": \"do_not_limit\"}", "reference_source": "{\"__current_case__\": 1, \"batchmode\": {\"__current_case__\": 0, \"input_bams\": {\"values\": [{\"id\": 348, \"src\": \"hda\"}]}, \"processmode\": \"individual\"}, \"ref_file\": {\"values\": [{\"id\": 349, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|batchmode|input_bams": {"id": "a7a65e481b711ac7", "src": "hda", "uuid": "68fce152-e077-461b-882f-4cee31ebedcd"}, "reference_source|ref_file": {"id": "27180e95bcf1e9cc", "src": "hda", "uuid": "cc2de2f2-86d9-4af0-9a93-2c08e4bfc2e7"}}, "outputs": {"output_vcf": {"id": "c6f3d382d4c978f9", "src": "hda", "uuid": "d5ddc6fd-2d39-4560-8446-f0e7070e221b"}}, "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": "2024-09-01 07:12:46", "plugin": "core", "name": "end_epoch", "raw_value": "1725174766.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 07:12:45", "plugin": "core", "name": "start_epoch", "raw_value": "1725174765.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "freebayes/1.3.6+galaxy0-3", "has_data": true, "data": {"tool_id": "freebayes", "tool_version": "1.3.6+galaxy0", "test_index": 3, "time_seconds": 39.682130575180054, "inputs": {"reference_source|batchmode|input_bams": {"src": "hda", "id": "504bb4797e958b58"}, "reference_source|batchmode|processmode": "individual", "reference_source|ref_file": {"src": "hda", "id": "ca81448756a13c7e"}, "reference_source|reference_source_selector": "history", "options_type|population_model|P": "1", "options_type|population_model|population_model_selector": "set", "options_type|options_type_selector": "full"}, "job": {"model_class": "Job", "id": "284dbc4a3c716da8", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T07:13:24.032017", "update_time": "2024-09-01T07:13:39.516039", "galaxy_version": "24.1", "external_id": "gxy-78pxg", "handler": null, "job_runner_name": null, "command_line": "ln -s -f '/galaxy/server/database/objects/1/2/8/dataset_128bc129-922f-443c-8b30-775195804385.dat' 'localref.fa' && samtools faidx 'localref.fa' 2>&1 || echo \"Error running samtools faidx for FreeBayes\" >&2 && ln -s -f '/galaxy/server/database/objects/8/0/6/dataset_80626689-9c05-48a7-bccd-882bb9c314ab.dat' 'b_0.bam' && ln -s -f '/galaxy/server/database/objects/_metadata_files/c/1/8/metadata_c187edff-4b28-4ec0-a5c9-5e360ea82a63.dat' 'b_0.bam.bai' && samtools view -H b_0.bam| grep '^@SQ' | cut -f 2- | awk '{ gsub(\"^SN:\",\"\",$1); gsub(\"^LN:\",\"\",$2); print $1\"\\t0\\t\"$2; }' >> regions_all.bed && sort -u regions_all.bed > regions_uniq.bed && mkdir vcf_output failed_alleles trace && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do echo \" freebayes --region '$i' --bam 'b_0.bam' --fasta-reference 'localref.fa' --vcf './vcf_output/part_$i.vcf' --theta 0.001 --ploidy 1 \"; done > freebayes_commands.sh && cat freebayes_commands.sh | parallel --will-cite -j ${GALAXY_SLOTS:-1} && grep \"^#\" \"./vcf_output/part_$i.vcf\" > header.txt && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do cat \"./vcf_output/part_$i.vcf\" | grep -v \"^#\" || true ; done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '/galaxy/server/database/objects/d/e/2/dataset_de24a4f9-e080-4324-8dec-7169782ceec7.dat'", "user_email": "tests@fake.org", "command_version": "1.3.6", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"O\": false, \"__current_case__\": 0, \"algorithmic_features\": {\"__current_case__\": 1, \"algorithmic_features_selector\": \"do_not_set\"}, \"allele_scope\": {\"__current_case__\": 1, \"allele_scope_selector\": \"do_not_set\"}, \"genotype_likelihoods\": {\"__current_case__\": 1, \"genotype_likelihoods_selector\": \"do_not_set\"}, \"input_filters\": {\"__current_case__\": 1, \"input_filters_selector\": \"do_not_set\"}, \"optional_inputs\": {\"__current_case__\": 1, \"optional_inputs_selector\": \"do_not_set\"}, \"options_type_selector\": \"full\", \"population_mappability_priors\": {\"__current_case__\": 1, \"population_mappability_priors_selector\": \"do_not_set\"}, \"population_model\": {\"J\": false, \"K\": false, \"P\": \"1\", \"T\": \"0.001\", \"__current_case__\": 0, \"population_model_selector\": \"set\"}, \"reference_allele\": {\"__current_case__\": 1, \"reference_allele_selector\": \"do_not_set\"}, \"reporting\": {\"__current_case__\": 1, \"reporting_selector\": \"do_not_set\"}}", "coverage_options": "{\"__current_case__\": 1, \"coverage_options_selector\": \"do_not_set\"}", "target_limit_type": "{\"__current_case__\": 0, \"target_limit_type_selector\": \"do_not_limit\"}", "reference_source": "{\"__current_case__\": 1, \"batchmode\": {\"__current_case__\": 0, \"input_bams\": {\"values\": [{\"id\": 351, \"src\": \"hda\"}]}, \"processmode\": \"individual\"}, \"ref_file\": {\"values\": [{\"id\": 352, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|batchmode|input_bams": {"id": "504bb4797e958b58", "src": "hda", "uuid": "80626689-9c05-48a7-bccd-882bb9c314ab"}, "reference_source|ref_file": {"id": "ca81448756a13c7e", "src": "hda", "uuid": "128bc129-922f-443c-8b30-775195804385"}}, "outputs": {"output_vcf": {"id": "17ef9b1db24a6c8f", "src": "hda", "uuid": "de24a4f9-e080-4324-8dec-7169782ceec7"}}, "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": "2024-09-01 07:13:26", "plugin": "core", "name": "end_epoch", "raw_value": "1725174806.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 07:13:25", "plugin": "core", "name": "start_epoch", "raw_value": "1725174805.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "freebayes/1.3.6+galaxy0-4", "has_data": true, "data": {"tool_id": "freebayes", "tool_version": "1.3.6+galaxy0", "test_index": 4, "time_seconds": 40.40553951263428, "inputs": {"reference_source|batchmode|input_bams": {"src": "hda", "id": "8664b7bbafaff2a1"}, "reference_source|batchmode|processmode": "individual", "reference_source|ref_file": {"src": "hda", "id": "ad5c26ca89afe4fc"}, "reference_source|reference_source_selector": "history", "coverage_options|min_coverage": "250", "coverage_options|coverage_options_selector": "set", "options_type|options_type_selector": "simple"}, "job": {"model_class": "Job", "id": "bd7bdbfc10eca8c1", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T07:14:03.822983", "update_time": "2024-09-01T07:14:20.020704", "galaxy_version": "24.1", "external_id": "gxy-t4mzb", "handler": null, "job_runner_name": null, "command_line": "ln -s -f '/galaxy/server/database/objects/5/0/0/dataset_500788e8-1bba-49a8-9446-d5bd8fbba5a9.dat' 'localref.fa' && samtools faidx 'localref.fa' 2>&1 || echo \"Error running samtools faidx for FreeBayes\" >&2 && ln -s -f '/galaxy/server/database/objects/1/7/d/dataset_17d4ab2f-93e7-407f-9f1f-756414165740.dat' 'b_0.bam' && ln -s -f '/galaxy/server/database/objects/_metadata_files/4/f/5/metadata_4f59f907-1718-486e-86d3-f28191c8d295.dat' 'b_0.bam.bai' && samtools view -H b_0.bam| grep '^@SQ' | cut -f 2- | awk '{ gsub(\"^SN:\",\"\",$1); gsub(\"^LN:\",\"\",$2); print $1\"\\t0\\t\"$2; }' >> regions_all.bed && sort -u regions_all.bed > regions_uniq.bed && mkdir vcf_output failed_alleles trace && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do echo \" freebayes --region '$i' --bam 'b_0.bam' --fasta-reference 'localref.fa' --vcf './vcf_output/part_$i.vcf' --min-coverage 250 --skip-coverage 0 --limit-coverage 0 \"; done > freebayes_commands.sh && cat freebayes_commands.sh | parallel --will-cite -j ${GALAXY_SLOTS:-1} && grep \"^#\" \"./vcf_output/part_$i.vcf\" > header.txt && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do cat \"./vcf_output/part_$i.vcf\" | grep -v \"^#\" || true ; done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '/galaxy/server/database/objects/e/a/6/dataset_ea63bfdf-3736-4bf5-a9c3-3e58b11b60e3.dat'", "user_email": "tests@fake.org", "command_version": "1.3.6", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"options_type_selector\": \"simple\"}", "coverage_options": "{\"__current_case__\": 0, \"coverage_options_selector\": \"set\", \"limit_coverage\": \"0\", \"min_coverage\": \"250\", \"skip_coverage\": \"0\"}", "target_limit_type": "{\"__current_case__\": 0, \"target_limit_type_selector\": \"do_not_limit\"}", "reference_source": "{\"__current_case__\": 1, \"batchmode\": {\"__current_case__\": 0, \"input_bams\": {\"values\": [{\"id\": 354, \"src\": \"hda\"}]}, \"processmode\": \"individual\"}, \"ref_file\": {\"values\": [{\"id\": 355, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|batchmode|input_bams": {"id": "8664b7bbafaff2a1", "src": "hda", "uuid": "17d4ab2f-93e7-407f-9f1f-756414165740"}, "reference_source|ref_file": {"id": "ad5c26ca89afe4fc", "src": "hda", "uuid": "500788e8-1bba-49a8-9446-d5bd8fbba5a9"}}, "outputs": {"output_vcf": {"id": "4cbabf389ab2ad1d", "src": "hda", "uuid": "ea63bfdf-3736-4bf5-a9c3-3e58b11b60e3"}}, "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": "2024-09-01 07:14:07", "plugin": "core", "name": "end_epoch", "raw_value": "1725174847.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 07:14:06", "plugin": "core", "name": "start_epoch", "raw_value": "1725174846.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "freebayes/1.3.6+galaxy0-5", "has_data": true, "data": {"tool_id": "freebayes", "tool_version": "1.3.6+galaxy0", "test_index": 5, "time_seconds": 31.023616790771484, "inputs": {"reference_source|batchmode|input_bams": {"src": "hda", "id": "86ac0b829e0ede78"}, "reference_source|batchmode|processmode": "individual", "reference_source|ref_file": {"src": "hda", "id": "0717868957076543"}, "reference_source|reference_source_selector": "history", "coverage_options|limit_coverage": "400", "coverage_options|coverage_options_selector": "set", "options_type|options_type_selector": "simple"}, "job": {"model_class": "Job", "id": "d52dd58fbb5ccf5d", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0", "state": "error", "exit_code": null, "create_time": "2024-09-01T07:14:45.276095", "update_time": "2024-09-01T07:14:51.268678", "galaxy_version": "24.1", "external_id": "gxy-7zl89", "handler": null, "job_runner_name": null, "command_line": "ln -s -f '/galaxy/server/database/objects/e/8/1/dataset_e8102b39-4eae-4c3f-b03d-c40a3fcebc2b.dat' 'localref.fa' && samtools faidx 'localref.fa' 2>&1 || echo \"Error running samtools faidx for FreeBayes\" >&2 && ln -s -f '/galaxy/server/database/objects/d/8/4/dataset_d8497632-be86-4cd4-9002-38bed82e337e.dat' 'b_0.bam' && ln -s -f '/galaxy/server/database/objects/_metadata_files/1/d/1/metadata_1d1cbf69-5d67-4e1d-8b1c-2896ea26c281.dat' 'b_0.bam.bai' && samtools view -H b_0.bam| grep '^@SQ' | cut -f 2- | awk '{ gsub(\"^SN:\",\"\",$1); gsub(\"^LN:\",\"\",$2); print $1\"\\t0\\t\"$2; }' >> regions_all.bed && sort -u regions_all.bed > regions_uniq.bed && mkdir vcf_output failed_alleles trace && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do echo \" freebayes --region '$i' --bam 'b_0.bam' --fasta-reference 'localref.fa' --vcf './vcf_output/part_$i.vcf' --min-coverage 0 --skip-coverage 0 --limit-coverage 400 \"; done > freebayes_commands.sh && cat freebayes_commands.sh | parallel --will-cite -j ${GALAXY_SLOTS:-1} && grep \"^#\" \"./vcf_output/part_$i.vcf\" > header.txt && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do cat \"./vcf_output/part_$i.vcf\" | grep -v \"^#\" || true ; done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '/galaxy/server/database/objects/f/a/6/dataset_fa616baa-d4f1-4b84-812b-14a39e432fab.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"options_type_selector\": \"simple\"}", "coverage_options": "{\"__current_case__\": 0, \"coverage_options_selector\": \"set\", \"limit_coverage\": \"400\", \"min_coverage\": \"0\", \"skip_coverage\": \"0\"}", "target_limit_type": "{\"__current_case__\": 0, \"target_limit_type_selector\": \"do_not_limit\"}", "reference_source": "{\"__current_case__\": 1, \"batchmode\": {\"__current_case__\": 0, \"input_bams\": {\"values\": [{\"id\": 357, \"src\": \"hda\"}]}, \"processmode\": \"individual\"}, \"ref_file\": {\"values\": [{\"id\": 358, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|batchmode|input_bams": {"id": "86ac0b829e0ede78", "src": "hda", "uuid": "d8497632-be86-4cd4-9002-38bed82e337e"}, "reference_source|ref_file": {"id": "0717868957076543", "src": "hda", "uuid": "e8102b39-4eae-4c3f-b03d-c40a3fcebc2b"}}, "outputs": {"output_vcf": {"id": "0f32c5a94b839107", "src": "hda", "uuid": "fa616baa-d4f1-4b84-812b-14a39e432fab"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "freebayes/1.3.6+galaxy0-6", "has_data": true, "data": {"tool_id": "freebayes", "tool_version": "1.3.6+galaxy0", "test_index": 6, "time_seconds": 40.82660436630249, "inputs": {"reference_source|batchmode|input_bams": {"src": "hda", "id": "79057f1bf008cb98"}, "reference_source|batchmode|processmode": "individual", "reference_source|ref_file": {"src": "hda", "id": "b00f9f6c26c8c7b7"}, "reference_source|reference_source_selector": "history", "coverage_options|skip_coverage": "100", "coverage_options|coverage_options_selector": "set", "options_type|options_type_selector": "simple"}, "job": {"model_class": "Job", "id": "8ae0eb027da1835a", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T07:15:16.292444", "update_time": "2024-09-01T07:15:31.961460", "galaxy_version": "24.1", "external_id": "gxy-zr6c9", "handler": null, "job_runner_name": null, "command_line": "ln -s -f '/galaxy/server/database/objects/9/7/2/dataset_972811f0-d37f-485e-ab2c-dba0c514cf4b.dat' 'localref.fa' && samtools faidx 'localref.fa' 2>&1 || echo \"Error running samtools faidx for FreeBayes\" >&2 && ln -s -f '/galaxy/server/database/objects/7/e/8/dataset_7e81ca3e-829f-4132-837d-222762c6fe64.dat' 'b_0.bam' && ln -s -f '/galaxy/server/database/objects/_metadata_files/7/e/b/metadata_7eb654d7-878f-45ae-8820-32b2cbc15aea.dat' 'b_0.bam.bai' && samtools view -H b_0.bam| grep '^@SQ' | cut -f 2- | awk '{ gsub(\"^SN:\",\"\",$1); gsub(\"^LN:\",\"\",$2); print $1\"\\t0\\t\"$2; }' >> regions_all.bed && sort -u regions_all.bed > regions_uniq.bed && mkdir vcf_output failed_alleles trace && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do echo \" freebayes --region '$i' --bam 'b_0.bam' --fasta-reference 'localref.fa' --vcf './vcf_output/part_$i.vcf' --min-coverage 0 --skip-coverage 100 --limit-coverage 0 \"; done > freebayes_commands.sh && cat freebayes_commands.sh | parallel --will-cite -j ${GALAXY_SLOTS:-1} && grep \"^#\" \"./vcf_output/part_$i.vcf\" > header.txt && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do cat \"./vcf_output/part_$i.vcf\" | grep -v \"^#\" || true ; done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '/galaxy/server/database/objects/6/a/b/dataset_6ab51a84-90be-471a-b87b-62798501aba0.dat'", "user_email": "tests@fake.org", "command_version": "1.3.6", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"options_type_selector\": \"simple\"}", "coverage_options": "{\"__current_case__\": 0, \"coverage_options_selector\": \"set\", \"limit_coverage\": \"0\", \"min_coverage\": \"0\", \"skip_coverage\": \"100\"}", "target_limit_type": "{\"__current_case__\": 0, \"target_limit_type_selector\": \"do_not_limit\"}", "reference_source": "{\"__current_case__\": 1, \"batchmode\": {\"__current_case__\": 0, \"input_bams\": {\"values\": [{\"id\": 360, \"src\": \"hda\"}]}, \"processmode\": \"individual\"}, \"ref_file\": {\"values\": [{\"id\": 361, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|batchmode|input_bams": {"id": "79057f1bf008cb98", "src": "hda", "uuid": "7e81ca3e-829f-4132-837d-222762c6fe64"}, "reference_source|ref_file": {"id": "b00f9f6c26c8c7b7", "src": "hda", "uuid": "972811f0-d37f-485e-ab2c-dba0c514cf4b"}}, "outputs": {"output_vcf": {"id": "e7d80b223b15163c", "src": "hda", "uuid": "6ab51a84-90be-471a-b87b-62798501aba0"}}, "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": "2024-09-01 07:15:18", "plugin": "core", "name": "end_epoch", "raw_value": "1725174918.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 07:15:18", "plugin": "core", "name": "start_epoch", "raw_value": "1725174918.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "freebayes/1.3.6+galaxy0-7", "has_data": true, "data": {"tool_id": "freebayes", "tool_version": "1.3.6+galaxy0", "test_index": 7, "time_seconds": 39.33661246299744, "inputs": {"reference_source|batchmode|input_bams": {"src": "hda", "id": "508be59732ad8f12"}, "reference_source|batchmode|processmode": "individual", "reference_source|ref_file": {"src": "hda", "id": "359da542978e9033"}, "reference_source|reference_source_selector": "history", "options_type|options_type_selector": "simple"}, "job": {"model_class": "Job", "id": "327188afff1e1a3d", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T07:15:56.132879", "update_time": "2024-09-01T07:16:11.431491", "galaxy_version": "24.1", "external_id": "gxy-d7sj8", "handler": null, "job_runner_name": null, "command_line": "ln -s -f '/galaxy/server/database/objects/1/8/d/dataset_18dcb913-c111-4028-b919-ed3701e8c841.dat' 'localref.fa' && samtools faidx 'localref.fa' 2>&1 || echo \"Error running samtools faidx for FreeBayes\" >&2 && ln -s -f '/galaxy/server/database/objects/5/4/f/dataset_54fa9f29-a78f-4495-b21f-a87ad4c44e10.dat' 'b_0.cram' && ln -s -f '/galaxy/server/database/objects/_metadata_files/0/d/d/metadata_0dd9fb43-809e-43b0-bd37-0a13f90a338b.dat' 'b_0.cram.crai' && samtools view -H b_0.cram| grep '^@SQ' | cut -f 2- | awk '{ gsub(\"^SN:\",\"\",$1); gsub(\"^LN:\",\"\",$2); print $1\"\\t0\\t\"$2; }' >> regions_all.bed && sort -u regions_all.bed > regions_uniq.bed && mkdir vcf_output failed_alleles trace && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do echo \" freebayes --region '$i' --bam 'b_0.cram' --fasta-reference 'localref.fa' --vcf './vcf_output/part_$i.vcf' \"; done > freebayes_commands.sh && cat freebayes_commands.sh | parallel --will-cite -j ${GALAXY_SLOTS:-1} && grep \"^#\" \"./vcf_output/part_$i.vcf\" > header.txt && for i in `cat regions_uniq.bed | awk '{print $1\":\"$2\"..\"$3}'`; do cat \"./vcf_output/part_$i.vcf\" | grep -v \"^#\" || true ; done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '/galaxy/server/database/objects/a/2/9/dataset_a291cf25-ea62-4e18-a869-779ae6128d5a.dat'", "user_email": "tests@fake.org", "command_version": "1.3.6", "params": {"__input_ext": "\"cram\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "options_type": "{\"__current_case__\": 1, \"options_type_selector\": \"simple\"}", "coverage_options": "{\"__current_case__\": 1, \"coverage_options_selector\": \"do_not_set\"}", "target_limit_type": "{\"__current_case__\": 0, \"target_limit_type_selector\": \"do_not_limit\"}", "reference_source": "{\"__current_case__\": 1, \"batchmode\": {\"__current_case__\": 0, \"input_bams\": {\"values\": [{\"id\": 363, \"src\": \"hda\"}]}, \"processmode\": \"individual\"}, \"ref_file\": {\"values\": [{\"id\": 364, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|batchmode|input_bams": {"id": "508be59732ad8f12", "src": "hda", "uuid": "54fa9f29-a78f-4495-b21f-a87ad4c44e10"}, "reference_source|ref_file": {"id": "359da542978e9033", "src": "hda", "uuid": "18dcb913-c111-4028-b919-ed3701e8c841"}}, "outputs": {"output_vcf": {"id": "887f6b956a93a847", "src": "hda", "uuid": "a291cf25-ea62-4e18-a869-779ae6128d5a"}}, "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": "2024-09-01 07:15:58", "plugin": "core", "name": "end_epoch", "raw_value": "1725174958.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 07:15:58", "plugin": "core", "name": "start_epoch", "raw_value": "1725174958.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "modify_loom/0.7.5+galaxy1-0", "has_data": true, "data": {"tool_id": "modify_loom", "tool_version": "0.7.5+galaxy1", "test_index": 0, "time_seconds": 51.730992794036865, "inputs": {"input": {"src": "hda", "id": "772a840bbe52b8de"}, "which_add|cols": {"src": "hda", "id": "7da7a29afe1bba80"}, "which_add|add_type": "cols"}, "job": {"model_class": "Job", "id": "8d7aaf7f3ff83e96", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T07:08:12.887164", "update_time": "2024-09-01T07:08:39.803002", "galaxy_version": "24.1", "external_id": "gxy-rfrw9", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/0/9/a/dataset_09aef566-b3a6-4495-966f-452353191b4c.dat' loom_add_out.loom && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/05631436cdf1/modify_loom/modify_loom.py' -f 'loom_add_out.loom' -a cols -c '/galaxy/server/database/objects/2/0/f/dataset_20f2de63-dbba-4d19-a686-ec8516ee9fd5.dat'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"loom\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "which_add": "{\"__current_case__\": 0, \"add_type\": \"cols\", \"cols\": {\"values\": [{\"id\": 333, \"src\": \"hda\"}]}}"}, "inputs": {"input": {"id": "772a840bbe52b8de", "src": "hda", "uuid": "09aef566-b3a6-4495-966f-452353191b4c"}, "which_add|cols": {"id": "7da7a29afe1bba80", "src": "hda", "uuid": "20f2de63-dbba-4d19-a686-ec8516ee9fd5"}}, "outputs": {"loomout": {"id": "879251e2e7333fce", "src": "hda", "uuid": "aa507466-ffdd-44e6-824c-f5459a41a8fa"}}, "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": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-01 07:08:24", "plugin": "core", "name": "end_epoch", "raw_value": "1725174504.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 07:08:22", "plugin": "core", "name": "start_epoch", "raw_value": "1725174502.0000000"}, {"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": "modify_loom/0.7.5+galaxy1-1", "has_data": true, "data": {"tool_id": "modify_loom", "tool_version": "0.7.5+galaxy1", "test_index": 1, "time_seconds": 41.328378438949585, "inputs": {"input": {"src": "hda", "id": "610f2f79a1b9306d"}, "which_add|rows": {"src": "hda", "id": "d9f49b881d7efefa"}, "which_add|add_type": "rows"}, "job": {"model_class": "Job", "id": "5063297f6a58e93c", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T07:09:03.965667", "update_time": "2024-09-01T07:09:21.161368", "galaxy_version": "24.1", "external_id": "gxy-dr9gx", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/e/1/2/dataset_e12e666d-dc9d-4573-b175-4ad7c5fe1a42.dat' loom_add_out.loom && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/05631436cdf1/modify_loom/modify_loom.py' -f 'loom_add_out.loom'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"loom\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "which_add": "{\"__current_case__\": 1, \"add_type\": \"rows\", \"rows\": {\"values\": [{\"id\": 336, \"src\": \"hda\"}]}}"}, "inputs": {"input": {"id": "610f2f79a1b9306d", "src": "hda", "uuid": "e12e666d-dc9d-4573-b175-4ad7c5fe1a42"}, "which_add|rows": {"id": "d9f49b881d7efefa", "src": "hda", "uuid": "27e75cbe-d60b-43c1-aea9-9855a3cd4fe7"}}, "outputs": {"loomout": {"id": "91b671824061ac44", "src": "hda", "uuid": "e238a3fb-6f11-42ca-a8c2-8b5f6e486d33"}}, "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": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-09-01 07:09:08", "plugin": "core", "name": "end_epoch", "raw_value": "1725174548.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 07:09:06", "plugin": "core", "name": "start_epoch", "raw_value": "1725174546.0000000"}, {"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": "modify_loom/0.7.5+galaxy1-2", "has_data": true, "data": {"tool_id": "modify_loom", "tool_version": "0.7.5+galaxy1", "test_index": 2, "time_seconds": 12.905650615692139, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "multiqc/1.9+galaxy1-0", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 0, "time_seconds": 138.64668440818787, "inputs": {"results_0|software_cond|input": {"src": "hda", "id": "4eb85bd6b7000860"}, "results_0|software_cond|software": "cutadapt", "results_1|software_cond|input": [{"src": "hda", "id": "699aa0be6b718c80"}, {"src": "hda", "id": "605b9c60d4868ba7"}], "results_1|software_cond|software": "fastp", "results_2|software_cond|output_0|type": "data", "results_2|software_cond|output_0|input": [{"src": "hda", "id": "3e66b905895552ba"}, {"src": "hda", "id": "7576055905cbfd53"}], "results_2|software_cond|software": "fastqc", "results_3|software_cond|input": {"src": "hda", "id": "fa5de90cc1bc3135"}, "results_3|software_cond|software": "flexbar", "results_4|software_cond|input": [{"src": "hda", "id": "e78e822db840a4cb"}, {"src": "hda", "id": "c43fa7dd8d328ba8"}, {"src": "hda", "id": "0220d52bbb525e17"}], "results_4|software_cond|software": "slamdunk", "results_5|software_cond|input": {"src": "hda", "id": "f368a0391184a0bc"}, "results_5|software_cond|software": "sortmerna", "results_6|software_cond|input": {"src": "hda", "id": "8ac2c7a3436e3123"}, "results_6|software_cond|software": "trimmomatic", "title": "Title of the report", "comment": "Commment for the report", "flat": true, "export": true, "saveLog": true}, "job": {"model_class": "Job", "id": "31f31cff9939c51a", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:36:03.341139", "update_time": "2024-09-01T06:37:07.979827", "galaxy_version": "24.1", "external_id": "gxy-krrk6", "handler": null, "job_runner_name": null, "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/cutadapt_0 && ln -s '/galaxy/server/database/objects/6/a/7/dataset_6a7acd6e-5193-4a2f-86fb-9bdd1c5d0f9f.dat' 'multiqc_WDir/cutadapt_0/cutadapt_txt.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/cutadapt_txt.txt' && grep -q \"This is cutadapt\" 'multiqc_WDir/cutadapt_0/cutadapt_txt.txt' || die \"'This is cutadapt' or 'You are running cutadapt' not found in the file\" && mkdir multiqc_WDir/fastp_1 && ln -s '/galaxy/server/database/objects/1/3/8/dataset_13885114-964b-45ae-81f5-3a79565cc478.dat' 'multiqc_WDir/fastp_1/fastp1_json_txtfastp.json' && grep -q \"report_title\" 'multiqc_WDir/fastp_1/fastp1_json_txtfastp.json' || die \"'report_title' or 'report_title' not found in the file\" && ln -s '/galaxy/server/database/objects/b/7/e/dataset_b7ef7801-8188-4692-9a4a-6d2d18457ca9.dat' 'multiqc_WDir/fastp_1/fastp2_json_txtfastp.json' && grep -q \"report_title\" 'multiqc_WDir/fastp_1/fastp2_json_txtfastp.json' || die \"'report_title' or 'report_title' not found in the file\" && mkdir multiqc_WDir/fastqc_2 && mkdir 'multiqc_WDir/fastqc_2/data_0' && mkdir 'multiqc_WDir/fastqc_2/data_0/file_0' && ln -s '/galaxy/server/database/objects/d/e/d/dataset_ded47f13-ebdc-4565-931f-6ed64885acf6.dat' 'multiqc_WDir/fastqc_2/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_2/data_0/file_1' && ln -s '/galaxy/server/database/objects/c/d/c/dataset_cdcc68a5-bd71-4832-831d-4f630e318d15.dat' 'multiqc_WDir/fastqc_2/data_0/file_1/fastqc_data.txt' && mkdir multiqc_WDir/flexbar_3 && grep -q 'flexible barcode and adapter removal' /galaxy/server/database/objects/f/d/5/dataset_fd533bfb-74d9-45a2-9f94-1afe9464399f.dat || die \"Module 'flexbar: 'flexible barcode and adapter removal' not found in the file 'flexbar_txt'\" && ln -s '/galaxy/server/database/objects/f/d/5/dataset_fd533bfb-74d9-45a2-9f94-1afe9464399f.dat' 'multiqc_WDir/flexbar_3/flexbar_txt' && mkdir multiqc_WDir/slamdunk_4 && grep -q '# slamdunk' /galaxy/server/database/objects/4/8/c/dataset_48ce7040-3908-41ef-9368-d24630e666d9.dat || die \"Module 'slamdunk: '# slamdunk' not found in the file 'slamdunk_summary_txt'\" && ln -s '/galaxy/server/database/objects/4/8/c/dataset_48ce7040-3908-41ef-9368-d24630e666d9.dat' 'multiqc_WDir/slamdunk_4/slamdunk_summary_txt' && grep -q '# slamdunk' /galaxy/server/database/objects/0/e/c/dataset_0ec1cf82-2309-43d9-bfcd-db2e23f15dce.dat || die \"Module 'slamdunk: '# slamdunk' not found in the file 'slamdunk_reads1_overallrates_csv'\" && ln -s '/galaxy/server/database/objects/0/e/c/dataset_0ec1cf82-2309-43d9-bfcd-db2e23f15dce.dat' 'multiqc_WDir/slamdunk_4/slamdunk_reads1_overallrates_csv' && grep -q '# slamdunk' /galaxy/server/database/objects/5/6/8/dataset_5689f419-898b-4064-a62f-f48ddc3f6cde.dat || die \"Module 'slamdunk: '# slamdunk' not found in the file 'slamdunk_reads2_overallrates_csv'\" && ln -s '/galaxy/server/database/objects/5/6/8/dataset_5689f419-898b-4064-a62f-f48ddc3f6cde.dat' 'multiqc_WDir/slamdunk_4/slamdunk_reads2_overallrates_csv' && mkdir multiqc_WDir/sortmerna_5 && grep -q 'Minimal SW score based on E-value' /galaxy/server/database/objects/c/4/e/dataset_c4e8fa90-5c25-4a74-875b-f15721b51f04.dat || die \"Module 'sortmerna: 'Minimal SW score based on E-value' not found in the file 'sortmerna_txt'\" && ln -s '/galaxy/server/database/objects/c/4/e/dataset_c4e8fa90-5c25-4a74-875b-f15721b51f04.dat' 'multiqc_WDir/sortmerna_5/sortmerna_txt' && mkdir multiqc_WDir/trimmomatic_6 && grep -q 'Trimmomatic' /galaxy/server/database/objects/b/a/0/dataset_ba05a082-a943-4fab-b1c8-aa5aeaf03fd6.dat || die \"Module 'trimmomatic: 'Trimmomatic' not found in the file 'trimmomatic_txt'\" && ln -s '/galaxy/server/database/objects/b/a/0/dataset_ba05a082-a943-4fab-b1c8-aa5aeaf03fd6.dat' 'multiqc_WDir/trimmomatic_6/trimmomatic_txt' && multiqc multiqc_WDir --filename \"report\" --title \"Title of the report\" --comment \"Commment for the report\" --flat --export", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "true", "export": "true", "flat": "true", "comment": "\"Commment for the report\"", "title": "\"Title of the report\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 5, \"input\": {\"values\": [{\"id\": 24, \"src\": \"hda\"}]}, \"software\": \"cutadapt\"}}, {\"__index__\": 1, \"software_cond\": {\"__current_case__\": 7, \"input\": {\"values\": [{\"id\": 25, \"src\": \"hda\"}, {\"id\": 26, \"src\": \"hda\"}]}, \"software\": \"fastp\"}}, {\"__index__\": 2, \"software_cond\": {\"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 27, \"src\": \"hda\"}, {\"id\": 28, \"src\": \"hda\"}]}, \"type\": \"data\"}], \"software\": \"fastqc\"}}, {\"__index__\": 3, \"software_cond\": {\"__current_case__\": 10, \"input\": {\"values\": [{\"id\": 29, \"src\": \"hda\"}]}, \"software\": \"flexbar\"}}, {\"__index__\": 4, \"software_cond\": {\"__current_case__\": 25, \"input\": {\"values\": [{\"id\": 30, \"src\": \"hda\"}, {\"id\": 31, \"src\": \"hda\"}, {\"id\": 32, \"src\": \"hda\"}]}, \"software\": \"slamdunk\"}}, {\"__index__\": 5, \"software_cond\": {\"__current_case__\": 27, \"input\": {\"values\": [{\"id\": 33, \"src\": \"hda\"}]}, \"software\": \"sortmerna\"}}, {\"__index__\": 6, \"software_cond\": {\"__current_case__\": 30, \"input\": {\"values\": [{\"id\": 34, \"src\": \"hda\"}]}, \"software\": \"trimmomatic\"}}]"}, "inputs": {"results_0|software_cond|input": {"id": "4eb85bd6b7000860", "src": "hda", "uuid": "6a7acd6e-5193-4a2f-86fb-9bdd1c5d0f9f"}, "results_0|software_cond|input1": {"id": "4eb85bd6b7000860", "src": "hda", "uuid": "6a7acd6e-5193-4a2f-86fb-9bdd1c5d0f9f"}, "results_1|software_cond|input2": {"id": "605b9c60d4868ba7", "src": "hda", "uuid": "b7ef7801-8188-4692-9a4a-6d2d18457ca9"}, "results_1|software_cond|input": {"id": "699aa0be6b718c80", "src": "hda", "uuid": "13885114-964b-45ae-81f5-3a79565cc478"}, "results_1|software_cond|input1": {"id": "699aa0be6b718c80", "src": "hda", "uuid": "13885114-964b-45ae-81f5-3a79565cc478"}, "results_2|software_cond|output_0|input": {"id": "3e66b905895552ba", "src": "hda", "uuid": "ded47f13-ebdc-4565-931f-6ed64885acf6"}, "results_2|software_cond|output_0|input1": {"id": "3e66b905895552ba", "src": "hda", "uuid": "ded47f13-ebdc-4565-931f-6ed64885acf6"}, "results_2|software_cond|output_0|input2": {"id": "7576055905cbfd53", "src": "hda", "uuid": "cdcc68a5-bd71-4832-831d-4f630e318d15"}, "results_3|software_cond|input": {"id": "fa5de90cc1bc3135", "src": "hda", "uuid": "fd533bfb-74d9-45a2-9f94-1afe9464399f"}, "results_3|software_cond|input1": {"id": "fa5de90cc1bc3135", "src": "hda", "uuid": "fd533bfb-74d9-45a2-9f94-1afe9464399f"}, "results_4|software_cond|input": {"id": "e78e822db840a4cb", "src": "hda", "uuid": "48ce7040-3908-41ef-9368-d24630e666d9"}, "results_4|software_cond|input1": {"id": "e78e822db840a4cb", "src": "hda", "uuid": "48ce7040-3908-41ef-9368-d24630e666d9"}, "results_4|software_cond|input2": {"id": "c43fa7dd8d328ba8", "src": "hda", "uuid": "0ec1cf82-2309-43d9-bfcd-db2e23f15dce"}, "results_6|software_cond|input": {"id": "8ac2c7a3436e3123", "src": "hda", "uuid": "ba05a082-a943-4fab-b1c8-aa5aeaf03fd6"}, "results_6|software_cond|input1": {"id": "8ac2c7a3436e3123", "src": "hda", "uuid": "ba05a082-a943-4fab-b1c8-aa5aeaf03fd6"}, "results_5|software_cond|input": {"id": "f368a0391184a0bc", "src": "hda", "uuid": "c4e8fa90-5c25-4a74-875b-f15721b51f04"}, "results_5|software_cond|input1": {"id": "f368a0391184a0bc", "src": "hda", "uuid": "c4e8fa90-5c25-4a74-875b-f15721b51f04"}, "results_4|software_cond|input3": {"id": "0220d52bbb525e17", "src": "hda", "uuid": "5689f419-898b-4064-a62f-f48ddc3f6cde"}}, "outputs": {"__new_primary_file_stats|trimmomatic__": {"id": "96378b79f935ff5d", "src": "hda", "uuid": "9f0aaf11-9dc1-4d83-9846-f7fed026d1d5"}, "__new_primary_file_stats|sources__": {"id": "9134d8030585c9b6", "src": "hda", "uuid": "644ef21c-f837-4443-8f39-ab71996b4330"}, "__new_primary_file_stats|sortmerna__": {"id": "4b9d0f9d3bd07264", "src": "hda", "uuid": "43fef372-a2cf-4e35-8c2c-c5fa6e7f39ae"}, "__new_primary_file_stats|slamdunk_readrates_plus__": {"id": "2129a7217775195d", "src": "hda", "uuid": "63290be3-e2dc-470a-ab05-4981b446bd46"}, "__new_primary_file_stats|slamdunk_readrates_minus__": {"id": "97959635f6439e5c", "src": "hda", "uuid": "dad1d48e-3cd2-4074-9887-2e5dfd01c67f"}, "__new_primary_file_stats|general_stats__": {"id": "8fc662fbc6bcde30", "src": "hda", "uuid": "9c072386-2b0e-4253-9508-d394bcbf4f81"}, "__new_primary_file_stats|flexbar__": {"id": "b16f60fa4a0293fe", "src": "hda", "uuid": "0c808ff6-5e9e-440e-84d1-56f7bbe76d9b"}, "__new_primary_file_stats|fastqc__": {"id": "5757eb3d49d1b901", "src": "hda", "uuid": "e24ded48-2cb5-4ef0-9919-f6665dd00a1a"}, "__new_primary_file_stats|fastp__": {"id": "003bb263eeefdeef", "src": "hda", "uuid": "896e51a9-4982-476d-8075-23d2f3b85224"}, "__new_primary_file_stats|cutadapt__": {"id": "fc7e18a9a612ec6a", "src": "hda", "uuid": "3ec843c4-877f-4e0c-bd08-46779641e4e2"}, "__new_primary_file_plots|trimmomatic_plot_1__": {"id": "7f089f6e9bfa5149", "src": "hda", "uuid": "8883024e-f4ab-4f9f-a0bf-917acf8f7ede"}, "__new_primary_file_plots|sortmerna-detailed-plot_1__": {"id": "9350901caecda29c", "src": "hda", "uuid": "dda999ab-c846-4c8a-ad39-950203fa75d1"}, "__new_primary_file_plots|overallratesplot_Plus_Strand___": {"id": "4e76c3858ff053da", "src": "hda", "uuid": "78d7dcb2-5a74-4d39-8f25-2720f047542e"}, "__new_primary_file_plots|overallratesplot_Minus_Strand_-__": {"id": "72e23cadb445b1c2", "src": "hda", "uuid": "4ef77909-3a14-4f8d-924d-59429e690c8a"}, "__new_primary_file_plots|flexbar_plot_1__": {"id": "ae1bbe5e4bf76959", "src": "hda", "uuid": "fb054a88-2f62-4147-9940-fa7b7b49d7a7"}, "__new_primary_file_plots|fastqc_sequence_duplication_levels_plot_1__": {"id": "6ed5d2b687499014", "src": "hda", "uuid": "117ceae8-5581-44c7-905e-1d96f80da47d"}, "__new_primary_file_plots|fastqc_sequence_counts_plot_1__": {"id": "e9ec43958db94025", "src": "hda", "uuid": "f727fa04-261d-4fb3-89ad-2925b170f18f"}, "__new_primary_file_plots|fastqc_per_sequence_quality_scores_plot_1__": {"id": "24ad18e51b66b35e", "src": "hda", "uuid": "c5b11d78-7376-46fa-88bf-8ce506255ca9"}, "__new_primary_file_plots|fastqc_per_sequence_gc_content_plot_Percentages__": {"id": "63fedbc370f6e2b4", "src": "hda", "uuid": "da80030b-e683-4c0d-9d26-f500e59a70a0"}, "__new_primary_file_plots|fastqc_per_sequence_gc_content_plot_Counts__": {"id": "3e444b52213641c9", "src": "hda", "uuid": "9a53df31-c238-493a-84e6-78dde7c2128c"}, "__new_primary_file_plots|fastqc_per_base_sequence_quality_plot_1__": {"id": "28aa9462084085ea", "src": "hda", "uuid": "09213598-33e6-4ec8-9ce2-51266ef364cf"}, "__new_primary_file_plots|fastqc_per_base_n_content_plot_1__": {"id": "9918673527029bc4", "src": "hda", "uuid": "c3f5066b-c89e-4ed1-96d8-3f30f7184611"}, "__new_primary_file_plots|fastp_filtered_reads_plot_1__": {"id": "8b425aef486bfe31", "src": "hda", "uuid": "9b80c11b-c037-4682-890a-44e02099037e"}, "__new_primary_file_plots|fastp-seq-quality-plot_Read_2_Before_filtering__": {"id": "46387bc733526dc0", "src": "hda", "uuid": "5f74f194-3075-435f-9086-dca621d1ff3d"}, "__new_primary_file_plots|fastp-seq-quality-plot_Read_2_After_filtering__": {"id": "c69410f7a914b46a", "src": "hda", "uuid": "e11feb70-139a-4af9-bddb-d37aea1b45c3"}, "__new_primary_file_plots|fastp-seq-quality-plot_Read_1_Before_filtering__": {"id": "0819d429057bf8a0", "src": "hda", "uuid": "1bb6b7c6-bf75-4654-9f37-340d7b9029f3"}, "__new_primary_file_plots|fastp-seq-quality-plot_Read_1_After_filtering__": {"id": "479d97ea1c916db2", "src": "hda", "uuid": "591154ad-e769-458b-8719-70097c266c53"}, "__new_primary_file_plots|fastp-seq-content-n-plot_Read_2_Before_filtering__": {"id": "5e5a97424da6c62a", "src": "hda", "uuid": "f01b0d2f-60d6-4e56-96e4-3166e14e981c"}, "__new_primary_file_plots|fastp-seq-content-n-plot_Read_2_After_filtering__": {"id": "a12ba167e91e005d", "src": "hda", "uuid": "59134958-e8d7-4e05-92cb-80f04b3ff5ab"}, "__new_primary_file_plots|fastp-seq-content-n-plot_Read_1_Before_filtering__": {"id": "a2d2642727f3065f", "src": "hda", "uuid": "187d8310-5b06-4c05-a487-4a04f0c9b3e8"}, "__new_primary_file_plots|fastp-seq-content-n-plot_Read_1_After_filtering__": {"id": "92b671c8c79cccb4", "src": "hda", "uuid": "62482791-1e02-4ed5-ba7e-ee6ed4e7fc39"}, "__new_primary_file_plots|fastp-seq-content-gc-plot_Read_2_Before_filtering__": {"id": "3f50a1e40454cbf1", "src": "hda", "uuid": "8f99d33e-de0d-45dc-89a4-5d5e68a22013"}, "__new_primary_file_plots|fastp-seq-content-gc-plot_Read_2_After_filtering__": {"id": "cd6dc1435b17bf3c", "src": "hda", "uuid": "29b6d9d4-a35c-4820-9bf7-bc57ba4c7b72"}, "__new_primary_file_plots|fastp-seq-content-gc-plot_Read_1_Before_filtering__": {"id": "3efcd2344b65bd51", "src": "hda", "uuid": "f4d8e02b-6abc-4f90-8302-719cbb21b66f"}, "__new_primary_file_plots|fastp-seq-content-gc-plot_Read_1_After_filtering__": {"id": "a776516a3ab01c8e", "src": "hda", "uuid": "eb22ac9b-da72-49b0-b92a-645cd54c5376"}, "__new_primary_file_plots|fastp-insert-size-plot_1__": {"id": "358bf293f6bd7c1f", "src": "hda", "uuid": "3922cf0f-1f61-44a1-9400-9860690b2d0e"}, "__new_primary_file_plots|fastp-duprates-plot_1__": {"id": "1e422eebd2ee4ea3", "src": "hda", "uuid": "47e10856-1845-4a43-be5f-2d8ebc63ae91"}, "__new_primary_file_plots|cutadapt_trimmed_sequences_plot_Obs_Exp__": {"id": "d88f6a5fa816379a", "src": "hda", "uuid": "b0288695-9ef6-48a8-ad55-9dfe2dddb163"}, "__new_primary_file_plots|cutadapt_trimmed_sequences_plot_Counts__": {"id": "d0cec92d73cc223c", "src": "hda", "uuid": "a9d8e1c3-3f19-43c4-a2c8-ee3ba7fe6b74"}, "log": {"id": "5e0de3ac9ddf08cd", "src": "hda", "uuid": "611b964c-44d3-429d-acd9-8303d4e73e8c"}, "html_report": {"id": "31f31cff9939c51a", "src": "hda", "uuid": "6afd1123-279f-43ab-93bc-e74386145820"}}, "copied_from_job_id": null, "output_collections": {"plots": {"src": "hdca", "id": "71d0106886a7baee"}, "stats": {"src": "hdca", "id": "0f5f5d39c9be041a"}}, "tool_stdout": "", "tool_stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/35/working/multiqc_WDir\n[INFO ] slamdunk : Found 2 reports\n[INFO ] cutadapt : Found 1 reports\n[WARNING] bargraph : Tried to make bar plot, but had no data\n[INFO ] flexbar : Found 1 logs\n[INFO ] trimmomatic : Found 1 logs\n[INFO ] sortmerna : Found 1 logs\n[INFO ] fastp : Found 2 reports\n[INFO ] fastqc : Found 2 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : Plots : report_plots\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/35/working/multiqc_WDir\n[INFO ] slamdunk : Found 2 reports\n[INFO ] cutadapt : Found 1 reports\n[WARNING] bargraph : Tried to make bar plot, but had no data\n[INFO ] flexbar : Found 1 logs\n[INFO ] trimmomatic : Found 1 logs\n[INFO ] sortmerna : Found 1 logs\n[INFO ] fastp : Found 2 reports\n[INFO ] fastqc : Found 2 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : Plots : report_plots\n[INFO ] multiqc : MultiQC complete\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "39 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "39.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:36:53", "plugin": "core", "name": "end_epoch", "raw_value": "1725172613.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:36:14", "plugin": "core", "name": "start_epoch", "raw_value": "1725172574.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "multiqc/1.9+galaxy1-0", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 0, "time_seconds": 32.69113278388977, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "multiqc/1.9+galaxy1-0", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 0, "time_seconds": 59.81124138832092, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "multiqc/1.9+galaxy1-1", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 1, "time_seconds": 34.79466128349304, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "multiqc/1.9+galaxy1-1", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 1, "time_seconds": 57.31094145774841, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "multiqc/1.9+galaxy1-1", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 1, "time_seconds": 80.88250374794006, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "multiqc/1.9+galaxy1-2", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 2, "time_seconds": 44.1508092880249, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "multiqc/1.9+galaxy1-2", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 2, "time_seconds": 191.0149281024933, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "multiqc/1.9+galaxy1-2", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 2, "time_seconds": 181.5015857219696, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "multiqc/1.9+galaxy1-3", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 3, "time_seconds": 177.03354024887085, "inputs": {"results_0|software_cond|plot_type": "linegraph", "results_0|software_cond|section_name": "BPC", "results_0|software_cond|title": "Base peak chromatogram", "results_0|software_cond|description": "Sum of intensity (Y) of the most intense peaks at each retention time(X)", "results_0|software_cond|xlab": "Retention Time", "results_0|software_cond|ylab": "Base Peak Intensity", "results_0|software_cond|input": [{"src": "hda", "id": "784cc9d3f6cae10e"}, {"src": "hda", "id": "9345e787ee1d96bf"}], "results_0|software_cond|software": "custom_content"}, "job": {"model_class": "Job", "id": "f65897791ea16e04", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:41:05.480645", "update_time": "2024-09-01T06:41:25.559957", "galaxy_version": "24.1", "external_id": "gxy-24rnl", "handler": null, "job_runner_name": null, "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/custom_content_0 && ln -s '/galaxy/server/database/objects/5/7/2/dataset_57270038-3a19-4873-a25c-8959487299fc.dat' 'multiqc_WDir/custom_content_0/file_0_0' && more /galaxy/server/database/objects/5/7/2/dataset_57270038-3a19-4873-a25c-8959487299fc.dat && ln -s '/galaxy/server/database/objects/1/c/0/dataset_1c0bf7b2-c399-40dd-9f28-c6c028269671.dat' 'multiqc_WDir/custom_content_0/file_0_1' && more /galaxy/server/database/objects/1/c/0/dataset_1c0bf7b2-c399-40dd-9f28-c6c028269671.dat && multiqc multiqc_WDir --filename \"report\" --config '/galaxy/server/database/jobs_directory/000/82/configs/tmparw237nt'", "user_email": "tests@fake.org", "command_version": "multiqc, version 1.9", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "false", "export": "false", "flat": "false", "comment": "\"\"", "title": "\"\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 32, \"description\": \"Sum of intensity (Y) of the most intense peaks at each retention time(X)\", \"input\": {\"values\": [{\"id\": 120, \"src\": \"hda\"}, {\"id\": 121, \"src\": \"hda\"}]}, \"plot_type\": \"linegraph\", \"section_name\": \"BPC\", \"software\": \"custom_content\", \"title\": \"Base peak chromatogram\", \"xlab\": \"Retention Time\", \"ylab\": \"Base Peak Intensity\"}}]"}, "inputs": {"results_0|software_cond|input": {"id": "784cc9d3f6cae10e", "src": "hda", "uuid": "57270038-3a19-4873-a25c-8959487299fc"}, "results_0|software_cond|input1": {"id": "784cc9d3f6cae10e", "src": "hda", "uuid": "57270038-3a19-4873-a25c-8959487299fc"}, "results_0|software_cond|input2": {"id": "9345e787ee1d96bf", "src": "hda", "uuid": "1c0bf7b2-c399-40dd-9f28-c6c028269671"}}, "outputs": {"html_report": {"id": "a6efb5c0e2a8d841", "src": "hda", "uuid": "895de052-8a5b-4b27-9458-003fe37b616c"}, "__new_primary_file_stats|sources__": {"id": "d69fe4bde36ad371", "src": "hda", "uuid": "5ed39ea7-9ed5-4278-9ce6-3d700bf24979"}}, "copied_from_job_id": null, "output_collections": {"stats": {"src": "hdca", "id": "19bc0e5055a63b46"}}, "tool_stdout": 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"tool_stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/82/working/multiqc_WDir\n[INFO ] custom_content : section_0: Found 2 samples (linegraph)\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stdout": 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"stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/82/working/multiqc_WDir\n[INFO ] custom_content : section_0: Found 2 samples (linegraph)\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "job_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": "2024-09-01 06:41:12", "plugin": "core", "name": "end_epoch", "raw_value": "1725172872.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:41:08", "plugin": "core", "name": "start_epoch", "raw_value": "1725172868.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output html_report: Test output file (report_manual_custom_content.html) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "multiqc/1.9+galaxy1-3", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 3, "time_seconds": 24.00064492225647, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "multiqc/1.9+galaxy1-3", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 3, "time_seconds": 45.934152603149414, "inputs": {"results_0|software_cond|plot_type": "linegraph", "results_0|software_cond|section_name": "BPC", "results_0|software_cond|title": "Base peak chromatogram", "results_0|software_cond|description": "Sum of intensity (Y) of the most intense peaks at each retention time(X)", "results_0|software_cond|xlab": "Retention Time", "results_0|software_cond|ylab": "Base Peak Intensity", "results_0|software_cond|input": [{"src": "hda", "id": "0a6fdadd6c20517d"}, {"src": "hda", "id": "fd640c1837446b76"}], "results_0|software_cond|software": "custom_content"}, "job": {"model_class": "Job", "id": "b5cf52fddd2eae10", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:55:35.521727", "update_time": "2024-09-01T06:55:55.651219", "galaxy_version": "24.1", "external_id": "gxy-fjgpl", "handler": null, "job_runner_name": null, "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/custom_content_0 && ln -s '/galaxy/server/database/objects/b/9/9/dataset_b9953e8b-f06b-4d62-8dc0-3e796f3e948a.dat' 'multiqc_WDir/custom_content_0/file_0_0' && more /galaxy/server/database/objects/b/9/9/dataset_b9953e8b-f06b-4d62-8dc0-3e796f3e948a.dat && ln -s '/galaxy/server/database/objects/4/0/a/dataset_40af9751-c185-4788-b071-55768dea65d7.dat' 'multiqc_WDir/custom_content_0/file_0_1' && more /galaxy/server/database/objects/4/0/a/dataset_40af9751-c185-4788-b071-55768dea65d7.dat && multiqc multiqc_WDir --filename \"report\" --config '/galaxy/server/database/jobs_directory/000/207/configs/tmpq8gcxoih'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "false", "export": "false", "flat": "false", "comment": "\"\"", "title": "\"\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 32, \"description\": \"Sum of intensity (Y) of the most intense peaks at each retention time(X)\", \"input\": {\"values\": [{\"id\": 270, \"src\": \"hda\"}, {\"id\": 271, \"src\": \"hda\"}]}, \"plot_type\": \"linegraph\", \"section_name\": \"BPC\", \"software\": \"custom_content\", \"title\": \"Base peak chromatogram\", \"xlab\": \"Retention Time\", \"ylab\": \"Base Peak Intensity\"}}]"}, "inputs": {"results_0|software_cond|input": {"id": "0a6fdadd6c20517d", "src": "hda", "uuid": "b9953e8b-f06b-4d62-8dc0-3e796f3e948a"}, "results_0|software_cond|input1": {"id": "0a6fdadd6c20517d", "src": "hda", "uuid": "b9953e8b-f06b-4d62-8dc0-3e796f3e948a"}, "results_0|software_cond|input2": {"id": "fd640c1837446b76", "src": "hda", "uuid": "40af9751-c185-4788-b071-55768dea65d7"}}, "outputs": {"__new_primary_file_stats|sources__": {"id": "9568984c6aaa2a59", "src": "hda", "uuid": "becd9c57-3f8b-4465-805d-0c441705696c"}, "html_report": {"id": "8ae0eb027da1835a", "src": "hda", "uuid": "acddc2f4-be2b-4652-b1b4-ec53aa6d6358"}}, "copied_from_job_id": null, "output_collections": {"stats": {"src": "hdca", "id": "7bff4c686fa3fe0d"}}, "tool_stdout": 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"tool_stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/207/working/multiqc_WDir\n[INFO ] custom_content : section_0: Found 2 samples (linegraph)\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stdout": 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"stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/207/working/multiqc_WDir\n[INFO ] custom_content : section_0: Found 2 samples (linegraph)\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:55:42", "plugin": "core", "name": "end_epoch", "raw_value": "1725173742.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:55:37", "plugin": "core", "name": "start_epoch", "raw_value": "1725173737.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "output_problems": ["Output html_report: Test output file (report_manual_custom_content.html) is missing. If you are using planemo, try adding --update_test_data to generate it."], "status": "failure"}}, {"id": "multiqc/1.9+galaxy1-4", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 4, "time_seconds": 53.54730224609375, "inputs": {"results_0|software_cond|output_0|type": "data", "results_0|software_cond|output_0|input": [{"src": "hda", "id": "9e67879db7815cd5"}, {"src": "hda", "id": "a53a933f8ff9995c"}], "results_0|software_cond|software": "fastqc", "title": "Title of the report", "comment": "Commment for the report", "flat": true, "export": true}, "job": {"model_class": "Job", "id": "64f98d71bc2bac30", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:41:50.825296", "update_time": "2024-09-01T06:42:18.835735", "galaxy_version": "24.1", "external_id": "gxy-5zczl", "handler": null, "job_runner_name": null, "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/fastqc_0 && mkdir 'multiqc_WDir/fastqc_0/data_0' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/galaxy/server/database/objects/8/4/c/dataset_84c055bd-655c-4f49-91b9-b5db90b307f4.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/galaxy/server/database/objects/a/e/1/dataset_ae19f1ba-be00-4743-b62b-c6766b39a80a.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' && multiqc multiqc_WDir --filename \"report\" --title \"Title of the report\" --comment \"Commment for the report\" --flat --export", "user_email": "tests@fake.org", "command_version": "multiqc, version 1.9", "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "false", "export": "true", "flat": "true", "comment": "\"Commment for the report\"", "title": "\"Title of the report\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 124, \"src\": \"hda\"}, {\"id\": 125, \"src\": \"hda\"}]}, \"type\": \"data\"}], \"software\": \"fastqc\"}}]"}, "inputs": {"results_0|software_cond|output_0|input": {"id": "9e67879db7815cd5", "src": "hda", "uuid": "84c055bd-655c-4f49-91b9-b5db90b307f4"}, "results_0|software_cond|output_0|input1": {"id": "9e67879db7815cd5", "src": "hda", "uuid": "84c055bd-655c-4f49-91b9-b5db90b307f4"}, "results_0|software_cond|output_0|input2": {"id": "a53a933f8ff9995c", "src": "hda", "uuid": "ae19f1ba-be00-4743-b62b-c6766b39a80a"}}, "outputs": {"html_report": {"id": "c336029ab95b1d6f", "src": "hda", "uuid": "6c1c6ed5-c127-45f8-854a-43a010665aa4"}, "__new_primary_file_plots|fastqc_per_base_n_content_plot_1__": {"id": "888078f7e2120d98", "src": "hda", "uuid": "23459840-2c71-4323-975e-a2d31278b42c"}, "__new_primary_file_plots|fastqc_per_base_sequence_quality_plot_1__": {"id": "40ec5ad3f0366ce1", "src": "hda", "uuid": "a2cb8f3e-3591-4b3b-b7d0-6b4dfe734ac1"}, "__new_primary_file_plots|fastqc_per_sequence_gc_content_plot_Counts__": {"id": "c4df62fdc7b2ddcd", "src": "hda", "uuid": "1fcaa1b4-59be-42a6-a609-7c5d42689005"}, "__new_primary_file_plots|fastqc_per_sequence_gc_content_plot_Percentages__": {"id": "653676bc098c5fdb", "src": "hda", "uuid": "fe5684cb-af4c-46c4-b49f-143469df12cb"}, "__new_primary_file_plots|fastqc_per_sequence_quality_scores_plot_1__": {"id": "2e579d560efcd06e", "src": "hda", "uuid": "f67ef0c9-048a-46f2-86e2-59b6b9c73bd8"}, "__new_primary_file_plots|fastqc_sequence_counts_plot_1__": {"id": "1562c02072c0e7c4", "src": "hda", "uuid": "dde985d9-aab4-490b-93fb-6b1ff4b5f25b"}, "__new_primary_file_plots|fastqc_sequence_duplication_levels_plot_1__": {"id": "092bba238028a448", "src": "hda", "uuid": "a615196e-55d9-4b61-ab59-4af3ab1d45fa"}, "__new_primary_file_stats|fastqc__": {"id": "a0b1a34be295a041", "src": "hda", "uuid": "2ba8d472-7ba1-45e8-96b1-298cf0ae26a9"}, "__new_primary_file_stats|general_stats__": {"id": "88559008d97b3013", "src": "hda", "uuid": "b5816eef-6204-4ae9-a530-fea6f9d6403e"}, "__new_primary_file_stats|sources__": {"id": "da616343dac2543f", "src": "hda", "uuid": "601d9073-59ca-42f6-ad15-27771adeeee6"}}, "copied_from_job_id": null, "output_collections": {"plots": {"src": "hdca", "id": "f4e8f03b50f50385"}, "stats": {"src": "hdca", "id": "a6c3c1dd0dbc7064"}}, "tool_stdout": "", "tool_stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/85/working/multiqc_WDir\n[INFO ] fastqc : Found 2 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : Plots : report_plots\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/85/working/multiqc_WDir\n[INFO ] fastqc : Found 2 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : Plots : report_plots\n[INFO ] multiqc : MultiQC complete\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "13 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "13.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:42:05", "plugin": "core", "name": "end_epoch", "raw_value": "1725172925.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:41:52", "plugin": "core", "name": "start_epoch", "raw_value": "1725172912.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "multiqc/1.9+galaxy1-4", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 4, "time_seconds": 54.68922519683838, "inputs": {"results_0|software_cond|output_0|type": "data", "results_0|software_cond|output_0|input": [{"src": "hda", "id": "baf966ba70779e05"}, {"src": "hda", "id": "dfd30aba3999ca69"}], "results_0|software_cond|software": "fastqc", "title": "Title of the report", "comment": "Commment for the report", "flat": true, "export": true}, "job": {"model_class": "Job", "id": "713a6342e499a9bf", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:48:34.697046", "update_time": "2024-09-01T06:49:03.405341", "galaxy_version": "24.1", "external_id": "gxy-n2ksz", "handler": null, "job_runner_name": null, "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/fastqc_0 && mkdir 'multiqc_WDir/fastqc_0/data_0' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/galaxy/server/database/objects/0/8/f/dataset_08f1b15e-6740-4648-9bd8-a54d0fe66330.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/galaxy/server/database/objects/9/1/4/dataset_9145d455-b15a-4d6c-b79d-071f90300621.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' && multiqc multiqc_WDir --filename \"report\" --title \"Title of the report\" --comment \"Commment for the report\" --flat --export", "user_email": "tests@fake.org", "command_version": "multiqc, version 1.9", "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "false", "export": "true", "flat": "true", "comment": "\"Commment for the report\"", "title": "\"Title of the report\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 198, \"src\": \"hda\"}, {\"id\": 199, \"src\": \"hda\"}]}, \"type\": \"data\"}], \"software\": \"fastqc\"}}]"}, "inputs": {"results_0|software_cond|output_0|input": {"id": "baf966ba70779e05", "src": "hda", "uuid": "08f1b15e-6740-4648-9bd8-a54d0fe66330"}, "results_0|software_cond|output_0|input1": {"id": "baf966ba70779e05", "src": "hda", "uuid": "08f1b15e-6740-4648-9bd8-a54d0fe66330"}, "results_0|software_cond|output_0|input2": {"id": "dfd30aba3999ca69", "src": "hda", "uuid": "9145d455-b15a-4d6c-b79d-071f90300621"}}, "outputs": {"html_report": {"id": "92545a1804560c88", "src": "hda", "uuid": "d1d778ed-81e0-4371-8f5d-cd7ac8b20c0b"}, "__new_primary_file_plots|fastqc_per_base_n_content_plot_1__": {"id": "15b628f3a8b45d2c", "src": "hda", "uuid": "72dff0cc-e73b-4094-b733-e2b224ab4c7f"}, "__new_primary_file_plots|fastqc_per_base_sequence_quality_plot_1__": {"id": "ec8f5b48e9d638bc", "src": "hda", "uuid": "9f75746b-4fce-4bfd-ba6f-d9d79ed39a26"}, "__new_primary_file_plots|fastqc_per_sequence_gc_content_plot_Counts__": {"id": "872f2e5ae242ac40", "src": "hda", "uuid": "1f27c5c5-f688-458f-99ef-1333c13876b7"}, "__new_primary_file_plots|fastqc_per_sequence_gc_content_plot_Percentages__": {"id": "e8daa2f7c7dd4915", "src": "hda", "uuid": "5fd00563-0f57-444c-91c3-6b53ea85de0b"}, "__new_primary_file_plots|fastqc_per_sequence_quality_scores_plot_1__": {"id": "7db6adfcfe2cf88f", "src": "hda", "uuid": "4dc11e55-5f95-41e5-9aad-ad0d9ef57558"}, "__new_primary_file_plots|fastqc_sequence_counts_plot_1__": {"id": "02653ed4bb020c6f", "src": "hda", "uuid": "60f91cfa-8a99-4175-99a8-092ef3c6c07a"}, "__new_primary_file_plots|fastqc_sequence_duplication_levels_plot_1__": {"id": "b5cf52fddd2eae10", "src": "hda", "uuid": "1168dd0a-471c-4e6f-94a3-01c84e4c7af8"}, "__new_primary_file_stats|fastqc__": {"id": "e785bde77f6c0c50", "src": "hda", "uuid": "7f008abc-c9d4-4667-b7f9-a8c61c71fb6b"}, "__new_primary_file_stats|general_stats__": {"id": "b14c4b460378e2ff", "src": "hda", "uuid": "dfd49ff2-078d-42c3-b126-8ef1c115e688"}, "__new_primary_file_stats|sources__": {"id": "8221186f614b82c0", "src": "hda", "uuid": "0c61aab4-5819-4d87-bed0-b6a18f5f25e2"}}, "copied_from_job_id": null, "output_collections": {"plots": {"src": "hdca", "id": "ac9b4d9a06230776"}, "stats": {"src": "hdca", "id": "65c15b69694655c0"}}, "tool_stdout": "", "tool_stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/147/working/multiqc_WDir\n[INFO ] fastqc : Found 2 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : Plots : report_plots\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/147/working/multiqc_WDir\n[INFO ] fastqc : Found 2 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : Plots : report_plots\n[INFO ] multiqc : MultiQC complete\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "13 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "13.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:48:49", "plugin": "core", "name": "end_epoch", "raw_value": "1725173329.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:48:36", "plugin": "core", "name": "start_epoch", "raw_value": "1725173316.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "multiqc/1.9+galaxy1-4", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 4, "time_seconds": 53.604230642318726, "inputs": {"results_0|software_cond|output_0|type": "data", "results_0|software_cond|output_0|input": [{"src": "hda", "id": "82cc754c1d951f3b"}, {"src": "hda", "id": "327188afff1e1a3d"}], "results_0|software_cond|software": "fastqc", "title": "Title of the report", "comment": "Commment for the report", "flat": true, "export": true}, "job": {"model_class": "Job", "id": "8221186f614b82c0", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:56:20.984262", "update_time": "2024-09-01T06:56:48.709937", "galaxy_version": "24.1", "external_id": "gxy-6h75p", "handler": null, "job_runner_name": null, "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/fastqc_0 && mkdir 'multiqc_WDir/fastqc_0/data_0' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/galaxy/server/database/objects/6/b/b/dataset_6bb8fe6c-15ae-4763-9bcd-146b41de77e6.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/galaxy/server/database/objects/e/5/b/dataset_e5ba7f90-d5de-4fea-96be-b2dd3e1bb3e4.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' && multiqc multiqc_WDir --filename \"report\" --title \"Title of the report\" --comment \"Commment for the report\" --flat --export", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"txt\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "false", "export": "true", "flat": "true", "comment": "\"Commment for the report\"", "title": "\"Title of the report\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 274, \"src\": \"hda\"}, {\"id\": 275, \"src\": \"hda\"}]}, \"type\": \"data\"}], \"software\": \"fastqc\"}}]"}, "inputs": {"results_0|software_cond|output_0|input": {"id": "82cc754c1d951f3b", "src": "hda", "uuid": "6bb8fe6c-15ae-4763-9bcd-146b41de77e6"}, "results_0|software_cond|output_0|input1": {"id": "82cc754c1d951f3b", "src": "hda", "uuid": "6bb8fe6c-15ae-4763-9bcd-146b41de77e6"}, "results_0|software_cond|output_0|input2": {"id": "327188afff1e1a3d", "src": "hda", "uuid": "e5ba7f90-d5de-4fea-96be-b2dd3e1bb3e4"}}, "outputs": {"__new_primary_file_stats|sources__": {"id": "452f1202fd627b61", "src": "hda", "uuid": "0a532b87-a61e-4065-8d27-a5635ee65a86"}, "__new_primary_file_stats|general_stats__": {"id": "581ba2a7c02bc8c2", "src": "hda", "uuid": "b565cf0f-85e4-45f1-9ec0-61c75a9203ef"}, "__new_primary_file_stats|fastqc__": {"id": "beb54766a4897cd4", "src": "hda", "uuid": "f7c7cd54-bd8f-4905-8185-a7df23ebe5a9"}, "__new_primary_file_plots|fastqc_sequence_duplication_levels_plot_1__": {"id": "d90f49ab235eaae5", "src": "hda", "uuid": "4553cc3e-a494-4cc4-8362-680461e110b3"}, "__new_primary_file_plots|fastqc_sequence_counts_plot_1__": {"id": "4789a0dc3a906884", "src": "hda", "uuid": "3c735340-e02c-411e-8d83-619150e16414"}, "__new_primary_file_plots|fastqc_per_sequence_quality_scores_plot_1__": {"id": "c10a472e563afa0b", "src": "hda", "uuid": "ac38aa2f-8e15-4d6d-9381-8e6591d54389"}, "__new_primary_file_plots|fastqc_per_sequence_gc_content_plot_Percentages__": {"id": "a663cbdc2ddcf8b2", "src": "hda", "uuid": "409ae8b4-4ba8-4916-a0ca-1e6fb0b5b0c2"}, "__new_primary_file_plots|fastqc_per_sequence_gc_content_plot_Counts__": {"id": "d7991a0e2a2ce0d7", "src": "hda", "uuid": "771a2555-46d0-41ef-9d79-4665ccb23cf9"}, "__new_primary_file_plots|fastqc_per_base_sequence_quality_plot_1__": {"id": "0fdb98639d6d499e", "src": "hda", "uuid": "6d0976e0-b902-4182-a0c6-e8461cc85c04"}, "__new_primary_file_plots|fastqc_per_base_n_content_plot_1__": {"id": "8a0841f2935fbf4b", "src": "hda", "uuid": "2d670bcf-b62b-4d65-baa3-08c7045ba58c"}, "html_report": {"id": "9daec2bfe02db058", "src": "hda", "uuid": "1fa5658e-1e4b-4e54-bece-37754318aac6"}}, "copied_from_job_id": null, "output_collections": {"plots": {"src": "hdca", "id": "747015e71ac9be6d"}, "stats": {"src": "hdca", "id": "291a07c912f667a1"}}, "tool_stdout": "", "tool_stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/210/working/multiqc_WDir\n[INFO ] fastqc : Found 2 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : Plots : report_plots\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/210/working/multiqc_WDir\n[INFO ] fastqc : Found 2 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : Plots : report_plots\n[INFO ] multiqc : MultiQC complete\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "13 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "13.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:56:35", "plugin": "core", "name": "end_epoch", "raw_value": "1725173795.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:56:22", "plugin": "core", "name": "start_epoch", "raw_value": "1725173782.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "multiqc/1.9+galaxy1-5", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 5, "time_seconds": 43.93703269958496, "inputs": {"results_0|software_cond|input": {"src": "hda", "id": "a7f57026c8e757f7"}, "results_0|software_cond|software": "pycoqc", "title": "Title of the report", "comment": "Commment for the report"}, "job": {"model_class": "Job", "id": "90d6c1306b660912", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:42:43.046574", "update_time": "2024-09-01T06:43:03.017996", "galaxy_version": "24.1", "external_id": "gxy-5nf6h", "handler": null, "job_runner_name": null, "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/pycoqc_0 && grep -q '\"pycoqc\":' /galaxy/server/database/objects/5/1/1/dataset_5110721b-a9ce-4a57-a9b0-189dce0ebae4.dat || die \"Module 'pycoqc: '\"pycoqc\":' not found in the file 'pycoqc_json'\" && ln -s '/galaxy/server/database/objects/5/1/1/dataset_5110721b-a9ce-4a57-a9b0-189dce0ebae4.dat' 'multiqc_WDir/pycoqc_0/pycoqc_json' && multiqc multiqc_WDir --filename \"report\" --title \"Title of the report\" --comment \"Commment for the report\"", "user_email": "tests@fake.org", "command_version": "multiqc, version 1.9", "params": {"__input_ext": "\"json\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "false", "export": "false", "flat": "false", "comment": "\"Commment for the report\"", "title": "\"Title of the report\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 19, \"input\": {\"values\": [{\"id\": 137, \"src\": \"hda\"}]}, \"software\": \"pycoqc\"}}]"}, "inputs": {"results_0|software_cond|input": {"id": "a7f57026c8e757f7", "src": "hda", "uuid": "5110721b-a9ce-4a57-a9b0-189dce0ebae4"}, "results_0|software_cond|input1": {"id": "a7f57026c8e757f7", "src": "hda", "uuid": "5110721b-a9ce-4a57-a9b0-189dce0ebae4"}}, "outputs": {"html_report": {"id": "6caa905440a7bbc7", "src": "hda", "uuid": "ae4d2842-c972-4843-b9b9-4cbe6e0e9639"}, "__new_primary_file_stats|general_stats__": {"id": "b6650900a132da8e", "src": "hda", "uuid": "4dae31a7-0025-464f-8eef-ce3f3e0add05"}, "__new_primary_file_stats|sources__": {"id": "9d8934708e5d0261", "src": "hda", "uuid": "bda96285-f271-4e36-9b08-64a34ed64afc"}}, "copied_from_job_id": null, "output_collections": {"stats": {"src": "hdca", "id": "b7124d2765df34d0"}}, "tool_stdout": "", "tool_stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/87/working/multiqc_WDir\n[INFO ] pycoqc : Found 1 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/87/working/multiqc_WDir\n[INFO ] pycoqc : Found 1 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:42:49", "plugin": "core", "name": "end_epoch", "raw_value": "1725172969.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:42:44", "plugin": "core", "name": "start_epoch", "raw_value": "1725172964.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "multiqc/1.9+galaxy1-5", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 5, "time_seconds": 42.28855347633362, "inputs": {"results_0|software_cond|input": {"src": "hda", "id": "0178724df954a766"}, "results_0|software_cond|software": "pycoqc", "title": "Title of the report", "comment": "Commment for the report"}, "job": {"model_class": "Job", "id": "02b7071018c5a5f0", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:49:27.549782", "update_time": "2024-09-01T06:49:46.381867", "galaxy_version": "24.1", "external_id": "gxy-6gqgf", "handler": null, "job_runner_name": null, "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/pycoqc_0 && grep -q '\"pycoqc\":' /galaxy/server/database/objects/b/6/d/dataset_b6da049d-8644-464f-b42d-a2a808220703.dat || die \"Module 'pycoqc: '\"pycoqc\":' not found in the file 'pycoqc_json'\" && ln -s '/galaxy/server/database/objects/b/6/d/dataset_b6da049d-8644-464f-b42d-a2a808220703.dat' 'multiqc_WDir/pycoqc_0/pycoqc_json' && multiqc multiqc_WDir --filename \"report\" --title \"Title of the report\" --comment \"Commment for the report\"", "user_email": "tests@fake.org", "command_version": "multiqc, version 1.9", "params": {"__input_ext": "\"json\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "false", "export": "false", "flat": "false", "comment": "\"Commment for the report\"", "title": "\"Title of the report\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 19, \"input\": {\"values\": [{\"id\": 211, \"src\": \"hda\"}]}, \"software\": \"pycoqc\"}}]"}, "inputs": {"results_0|software_cond|input": {"id": "0178724df954a766", "src": "hda", "uuid": "b6da049d-8644-464f-b42d-a2a808220703"}, "results_0|software_cond|input1": {"id": "0178724df954a766", "src": "hda", "uuid": "b6da049d-8644-464f-b42d-a2a808220703"}}, "outputs": {"html_report": {"id": "ad76ce97aaa575c4", "src": "hda", "uuid": "39e872cb-573d-4f23-b9ad-2c2f3a438a07"}, "__new_primary_file_stats|general_stats__": {"id": "a51f03954997a9af", "src": "hda", "uuid": "09c7603c-8f28-45b0-a0eb-4cad5305d5b7"}, "__new_primary_file_stats|sources__": {"id": "0d3c5de3e5c91d32", "src": "hda", "uuid": "e84a8919-fed5-4098-aacb-a1ca790ff654"}}, "copied_from_job_id": null, "output_collections": {"stats": {"src": "hdca", "id": "0b8dda5741c86c37"}}, "tool_stdout": "", "tool_stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/149/working/multiqc_WDir\n[INFO ] pycoqc : Found 1 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/149/working/multiqc_WDir\n[INFO ] pycoqc : Found 1 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:49:33", "plugin": "core", "name": "end_epoch", "raw_value": "1725173373.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:49:28", "plugin": "core", "name": "start_epoch", "raw_value": "1725173368.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "multiqc/1.9+galaxy1-5", "has_data": true, "data": {"tool_id": "multiqc", "tool_version": "1.9+galaxy1", "test_index": 5, "time_seconds": 43.53632211685181, "inputs": {"results_0|software_cond|input": {"src": "hda", "id": "06416ac3afaea875"}, "results_0|software_cond|software": "pycoqc", "title": "Title of the report", "comment": "Commment for the report"}, "job": {"model_class": "Job", "id": "ad76ce97aaa575c4", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:57:12.767751", "update_time": "2024-09-01T06:57:32.908457", "galaxy_version": "24.1", "external_id": "gxy-x8gg4", "handler": null, "job_runner_name": null, "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/pycoqc_0 && grep -q '\"pycoqc\":' /galaxy/server/database/objects/b/3/d/dataset_b3d5b358-9d05-4532-85e6-05a51c576442.dat || die \"Module 'pycoqc: '\"pycoqc\":' not found in the file 'pycoqc_json'\" && ln -s '/galaxy/server/database/objects/b/3/d/dataset_b3d5b358-9d05-4532-85e6-05a51c576442.dat' 'multiqc_WDir/pycoqc_0/pycoqc_json' && multiqc multiqc_WDir --filename \"report\" --title \"Title of the report\" --comment \"Commment for the report\"", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"json\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "saveLog": "false", "export": "false", "flat": "false", "comment": "\"Commment for the report\"", "title": "\"Title of the report\"", "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 19, \"input\": {\"values\": [{\"id\": 287, \"src\": \"hda\"}]}, \"software\": \"pycoqc\"}}]"}, "inputs": {"results_0|software_cond|input": {"id": "06416ac3afaea875", "src": "hda", "uuid": "b3d5b358-9d05-4532-85e6-05a51c576442"}, "results_0|software_cond|input1": {"id": "06416ac3afaea875", "src": "hda", "uuid": "b3d5b358-9d05-4532-85e6-05a51c576442"}}, "outputs": {"__new_primary_file_stats|sources__": {"id": "429f2d046331bd2b", "src": "hda", "uuid": "6a6b0962-58c3-45e3-81cf-454d6b3ab336"}, "__new_primary_file_stats|general_stats__": {"id": "492876b2b8d7fa19", "src": "hda", "uuid": "33c7a2ed-f375-4d77-b33a-28e6e0dbfb80"}, "html_report": {"id": "b73db2180733969f", "src": "hda", "uuid": "2e522391-9313-44c1-81a2-f3abd3ae8e36"}}, "copied_from_job_id": null, "output_collections": {"stats": {"src": "hdca", "id": "039b04b47906a4fd"}}, "tool_stdout": "", "tool_stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/212/working/multiqc_WDir\n[INFO ] pycoqc : Found 1 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[WARNING] multiqc : MultiQC Version v1.24.1 now available!\n[INFO ] multiqc : This is MultiQC v1.9\n[INFO ] multiqc : Template : default\n[INFO ] multiqc : Report title: Title of the report\n[INFO ] multiqc : Searching : /galaxy/server/database/jobs_directory/000/212/working/multiqc_WDir\n[INFO ] pycoqc : Found 1 reports\n[INFO ] multiqc : Compressing plot data\n[INFO ] multiqc : Report : report.html\n[INFO ] multiqc : Data : report_data\n[INFO ] multiqc : MultiQC complete\n", "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": "2024-09-01 06:57:19", "plugin": "core", "name": "end_epoch", "raw_value": "1725173839.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:57:15", "plugin": "core", "name": "start_epoch", "raw_value": "1725173835.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "nanoplot/1.28.2+galaxy1-0", "has_data": true, "data": {"tool_id": "nanoplot", "tool_version": "1.28.2+galaxy1", "test_index": 0, "time_seconds": 88.81571555137634, "inputs": {"mode|reads|files": {"src": "hda", "id": "1dc43afa8922e2b5"}, "mode|reads|type": "fastq_rich", "mode|choice": "batch", "filter|downsample": "800", "customization|plots": ["hex", "kde"]}, "job": {"model_class": "Job", "id": "0d3c5de3e5c91d32", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:57:59.146581", "update_time": "2024-09-01T06:59:02.237909", "galaxy_version": "24.1", "external_id": "gxy-2t2zb", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/0/4/4/dataset_0446a401-1bfa-4952-a560-598bde00e5d0.dat' './read.fastq.gz' && NanoPlot --threads ${GALAXY_SLOTS:-4} --fastq_rich read.fastq.gz --downsample 800 --format png --plots hex kde -o '.'", "user_email": "tests@fake.org", "command_version": "NanoPlot 1.28.2", "params": {"__input_ext": "\"fastq.gz\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "customization": "{\"N50\": false, \"color\": null, \"format\": \"png\", \"plots\": [\"hex\", \"kde\"]}", "filter": "{\"alength\": false, \"barcoded\": false, \"downsample\": \"800\", \"drop_outliers\": false, \"loglength\": false, \"maxlength\": \"\", \"minlength\": \"\", \"minqual\": \"\", \"percentqual\": false, \"readtype\": null}", "mode": "{\"__current_case__\": 0, \"choice\": \"batch\", \"reads\": {\"__current_case__\": 2, \"files\": {\"values\": [{\"id\": 291, \"src\": \"hda\"}]}, \"type\": \"fastq_rich\"}}"}, "inputs": {"mode|reads|files": {"id": "1dc43afa8922e2b5", "src": "hda", "uuid": "0446a401-1bfa-4952-a560-598bde00e5d0"}}, "outputs": {"log_read_length": {"id": "8bed9897bcb159ee", "src": "hda", "uuid": "e42d1713-4129-4dd2-8391-11a4a4cea496"}, "read_length": {"id": "7e74efd36746412c", "src": "hda", "uuid": "431aa0da-9560-453b-8143-da74ae4f9af9"}, "nanostats_post_filtering": {"id": "2a40b2de8c94c1df", "src": "hda", "uuid": "c2a92016-856a-4fd1-a6c0-3530cd58b989"}, "nanostats": {"id": "b91ae4f8150c7354", "src": "hda", "uuid": "8a1e0e0f-d3c9-4548-aa5b-7d7cb5403a39"}, "output_html": {"id": "ae9d5c9f144658d3", "src": "hda", "uuid": "470a77ba-8c83-4b9c-b354-e61061aebc1c"}}, "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": "21 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "21.0000000"}, {"title": "Job End Time", "value": "2024-09-01 06:58:43", "plugin": "core", "name": "end_epoch", "raw_value": "1725173923.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 06:58:22", "plugin": "core", "name": "start_epoch", "raw_value": "1725173902.0000000"}, {"title": "Memory Allocated (MB)", "value": "12884", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12884.0000000"}, {"title": "Cores Allocated", "value": "2", "plugin": "core", "name": "galaxy_slots", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "nanoplot/1.28.2+galaxy1-1", "has_data": true, "data": {"tool_id": "nanoplot", "tool_version": "1.28.2+galaxy1", "test_index": 1, "time_seconds": 80.11029434204102, "inputs": {"mode|reads|files": {"src": "hda", "id": "d6d6a5bf4c803799"}, "mode|reads|type": "bam", "mode|choice": "combined", "filter|maxlength": "2000", "customization|color": "yellow", "customization|format": "svg"}, "job": {"model_class": "Job", "id": "c4cb064e29a3e0f7", "history_id": "0f5f5d39c9be041a", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-01T06:59:29.944673", "update_time": "2024-09-01T07:00:22.382039", "galaxy_version": "24.1", "external_id": "gxy-jzbph", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/b/1/6/dataset_b16996be-95a8-49ac-840e-e7ba393bac97.dat' './read_0.bam' && NanoPlot --threads ${GALAXY_SLOTS:-4} --bam read_0.bam --maxlength 2000 --color yellow --format svg -o '.'", "user_email": "tests@fake.org", "command_version": "NanoPlot 1.28.2", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "customization": "{\"N50\": false, \"color\": \"yellow\", \"format\": \"svg\", \"plots\": null}", "filter": "{\"alength\": false, \"barcoded\": false, \"downsample\": \"\", \"drop_outliers\": false, \"loglength\": false, \"maxlength\": \"2000\", \"minlength\": \"\", \"minqual\": \"\", \"percentqual\": false, \"readtype\": null}", "mode": "{\"__current_case__\": 1, \"choice\": \"combined\", \"reads\": {\"__current_case__\": 5, \"files\": {\"values\": [{\"id\": 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To cite Bioconductor, see\n 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\n\nAttaching package: \u2018Biobase\u2019\n\nThe following object is masked from \u2018package:MatrixGenerics\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n anyMissing, rowMedians\n\nLoading required package: rhdf5\nLoading required package: BiocIO\nLoading required package: scuttle\nLoading required package: ggplot2\nSaving 7 x 7 in image\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Loading required package: S4Vectors\nLoading required package: stats4\nLoading required package: BiocGenerics\n\nAttaching package: \u2018BiocGenerics\u2019\n\nThe following objects are masked from \u2018package:stats\u2019:\n\n IQR, mad, sd, var, xtabs\n\nThe following objects are masked from \u2018package:base\u2019:\n\n anyDuplicated, append, as.data.frame, basename, cbind, colnames,\n dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,\n grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,\n order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\n rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,\n union, unique, unsplit, which.max, which.min\n\n\nAttaching package: \u2018S4Vectors\u2019\n\nThe following objects are masked from \u2018package:base\u2019:\n\n expand.grid, I, unname\n\nLoading required package: SingleCellExperiment\nLoading required package: SummarizedExperiment\nLoading required package: MatrixGenerics\nLoading required package: matrixStats\n\nAttaching package: \u2018MatrixGenerics\u2019\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,\n colCounts, colCummaxs, colCummins, colCumprods, colCumsums,\n colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,\n colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,\n colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,\n colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,\n colWeightedMeans, colWeightedMedians, colWeightedSds,\n colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,\n rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,\n rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,\n rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,\n rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,\n rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,\n rowWeightedMads, rowWeightedMeans, rowWeightedMedians,\n rowWeightedSds, rowWeightedVars\n\nLoading required package: GenomicRanges\nLoading required package: IRanges\nLoading required package: GenomeInfoDb\nLoading required package: Biobase\nWelcome to Bioconductor\n\n Vignettes contain introductory material; view with\n 'browseVignettes()'. To cite Bioconductor, see\n 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\n\nAttaching package: \u2018Biobase\u2019\n\nThe following object is masked from \u2018package:MatrixGenerics\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n anyMissing, rowMedians\n\nLoading required package: rhdf5\nLoading required package: BiocIO\nLoading required package: scuttle\nLoading required package: ggplot2\nSaving 7 x 7 in image\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "12 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "12.0000000"}, {"title": "Job End Time", "value": "2024-09-01 07:10:35", "plugin": "core", "name": "end_epoch", "raw_value": "1725174635.0000000"}, {"title": "Job Start Time", "value": "2024-09-01 07:10:23", "plugin": "core", "name": "start_epoch", "raw_value": "1725174623.0000000"}, {"title": "Memory Allocated (MB)", "value": 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