diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md index ba913035f..5f3a67b4b 100644 --- a/reports/anvil-edge/README.md +++ b/reports/anvil-edge/README.md @@ -13,4 +13,4 @@ After each successful deployment, automated tool tests are also run against the Latest tool tests for each chunk: -
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 16 06:27:02 2024Mon Sep 09 06:26:24 2024
1ToolsetMon Sep 16 18:32:01 2024Mon Sep 09 18:31:59 2024
2ToolsetTue Sep 17 06:26:34 2024Tue Sep 10 06:27:04 2024
3ToolsetTue Sep 17 18:34:01 2024Tue Sep 10 18:32:07 2024
4ToolsetWed Sep 18 06:26:06 2024Wed Sep 11 06:26:47 2024
5ToolsetWed Sep 18 18:32:06 2024Wed Sep 11 18:32:01 2024
6ToolsetThu Sep 19 06:26:39 2024Thu Sep 12 06:26:50 2024
7ToolsetThu Sep 19 18:31:09 2024Thu Sep 12 18:33:11 2024
8ToolsetFri Sep 20 06:25:56 2024Fri Sep 13 06:26:17 2024
9ToolsetFri Sep 20 18:32:50 2024Fri Sep 13 18:32:19 2024
10ToolsetSat Sep 21 06:25:16 2024Sat Sep 14 06:24:56 2024
11ToolsetSat Sep 21 18:31:38 2024Sat Sep 14 18:30:22 2024
12ToolsetSun Sep 22 06:25:20 2024Sun Sep 15 06:25:35 2024
13ToolsetSun Sep 15 18:32:12 2024Sun Sep 08 18:31:42 2024
+
Chunk IDTool ListLatest reportPrevious report
0ToolsetMon Sep 16 06:27:02 2024Mon Sep 09 06:26:24 2024
1ToolsetMon Sep 16 18:32:01 2024Mon Sep 09 18:31:59 2024
2ToolsetTue Sep 17 06:26:34 2024Tue Sep 10 06:27:04 2024
3ToolsetTue Sep 17 18:34:01 2024Tue Sep 10 18:32:07 2024
4ToolsetWed Sep 18 06:26:06 2024Wed Sep 11 06:26:47 2024
5ToolsetWed Sep 18 18:32:06 2024Wed Sep 11 18:32:01 2024
6ToolsetThu Sep 19 06:26:39 2024Thu Sep 12 06:26:50 2024
7ToolsetThu Sep 19 18:31:09 2024Thu Sep 12 18:33:11 2024
8ToolsetFri Sep 20 06:25:56 2024Fri Sep 13 06:26:17 2024
9ToolsetFri Sep 20 18:32:50 2024Fri Sep 13 18:32:19 2024
10ToolsetSat Sep 21 06:25:16 2024Sat Sep 14 06:24:56 2024
11ToolsetSat Sep 21 18:31:38 2024Sat Sep 14 18:30:22 2024
12ToolsetSun Sep 22 06:25:20 2024Sun Sep 15 06:25:35 2024
13ToolsetSun Sep 22 18:31:24 2024Sun Sep 15 18:32:12 2024
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json index 6bc9f51b6..9e9b92b53 100644 --- a/reports/anvil-edge/tool-tests/chunks.json +++ b/reports/anvil-edge/tool-tests/chunks.json @@ -77,11 +77,11 @@ "date2": "Sun Sep 15 06:25:35 2024" }, "13": { - "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-15-18-16-1/results.html", - "date1": "Sun Sep 15 18:32:12 2024", - "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-15-18-16-1/tools.yml", - "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-08-18-16-1/results.html", - "date2": "Sun Sep 08 18:31:42 2024" + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/results.html", + "date1": "Sun Sep 22 18:31:24 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/tools.yml", + "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-15-18-16-1/results.html", + "date2": "Sun Sep 15 18:32:12 2024" }, "0": { "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-16-06-12-1/results.html", diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/chunk.json new file mode 100644 index 000000000..a299c129f --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/chunk.json @@ -0,0 +1,7 @@ +{ + "13": { + "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/results.html", + "date1": "Sun Sep 22 18:31:24 2024", + "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/tools.yml" + } +} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/chunk.txt new file mode 100644 index 000000000..f530f9f03 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/chunk.txt @@ -0,0 +1,25 @@ +-t deeptools_plot_heatmap --tool-version a4dfb122e52b +-t deeptools_plot_profile --tool-version c361b12d207a +-t fastp --tool-version dbf9c561ef29 +-t rgrnastar --tool-version c772497b2c32 +-t rgrnastar --tool-version 2055c2667eb3 +-t rgrnastar --tool-version 980d2a2e1180 +-t poretools_events --tool-version 28d7819c312f +-t pharmcat --tool-version d67642a21a1d +-t qualimap_bamqc --tool-version 19ece8afbaab +-t samtools_stats --tool-version 145f6d74ff5e +-t samtools_stats --tool-version 24c5d43cb545 +-t filter_on_md --tool-version ac70bfaf1224 +-t dropletutils --tool-version a9caad671439 +-t dropletutils --tool-version 2c1200fba922 +-t scater_filter --tool-version 652923ce664f +-t scater_filter --tool-version b7ea9f09c02f +-t sceasy_convert --tool-version f62bc418173f +-t scanpy_find_markers --tool-version eb01a7e59e9a +-t scanpy_find_markers --tool-version f04dd4e5b6a7 +-t reshape2_cast --tool-version d3b66a3a08ca +-t snpsift_genesets --tool-version d12a810c837e +-t bcftools_plugin_setgt --tool-version 8abfcd1a6949 +-t bcftools_call --tool-version 072f606e2e69 +-t vcfbreakcreatemulti --tool-version 9fd5d91eb91b +-t vcfselectsamples --tool-version 2ba3b87f904f diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/00bf5e33f5f60a84.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/00bf5e33f5f60a84.json new file mode 100644 index 000000000..b80f983f1 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/00bf5e33f5f60a84.json @@ -0,0 +1,60 @@ +{ + "model_class": "Job", + "id": "00bf5e33f5f60a84", + "history_id": "b2116f9eb07476cf", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", + "state": "error", + "exit_code": null, + "create_time": "2024-09-22T19:16:09.360909", + "update_time": "2024-09-22T19:16:29.622402", + "galaxy_version": "24.1", + "external_id": "gxy-r4m44", + "handler": null, + "job_runner_name": null, + "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/a9caad671439/dropletutils/scripts/dropletutils.Rscript' '/galaxy/server/database/jobs_directory/000/157/configs/tmpfdt0g2xt'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"h5\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "seed": "\"100\"", + "operation": "{\"__current_case__\": 0, \"method\": {\"__current_case__\": 1, \"fdr_thresh\": \"0.02\", \"lower\": \"150\", \"use\": \"emptydrops\"}, \"outformat\": \"h5\", \"use\": \"filter\"}", + "tenx_format": "{\"__current_case__\": 1, \"input\": {\"values\": [{\"id\": 239, \"src\": \"hda\"}]}, \"use\": \"h5\"}" + }, + "inputs": { + "tenx_format|input": { + "id": "2e82e628690af495", + "src": "hda", + "uuid": "55edb90b-5bb7-4496-a18a-d9fa3f535a94" + } + }, + "outputs": { + "fileout_h5": { + "id": "24cc1dc6eaa8876f", + "src": "hda", + "uuid": "22598fa7-3f7c-4764-842e-089622eb9d10" + }, + "plot": { + "id": "807bfe01e9a68c8e", + "src": "hda", + "uuid": "7906c188-bd71-4f7a-9151-2df05203f29e" + }, + "table": { + "id": "a9e73c1f2c590fd8", + "src": "hda", + "uuid": "c5d79519-4992-4643-bfff-73421ab8e541" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "[1] \"Cell Library Size Distribution:\"\n Min. 1st Qu. Median Mean 3rd Qu. Max. \n 0.0 8.0 20.0 114.3 46.0 2347.0 \n", + "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 954\nCells and Limited: 85\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "[1] \"Cell Library Size Distribution:\"\n Min. 1st Qu. Median Mean 3rd Qu. Max. \n 0.0 8.0 20.0 114.3 46.0 2347.0 \n", + "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 954\nCells and Limited: 85\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/23fa96fce5eed89f.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/23fa96fce5eed89f.json new file mode 100644 index 000000000..dec55cf5e --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/23fa96fce5eed89f.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "23fa96fce5eed89f", + "history_id": "b2116f9eb07476cf", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-22T19:28:21.683999", + "update_time": "2024-09-22T19:28:34.511928", + "galaxy_version": "24.1", + "external_id": "gxy-jmt8r", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/197/registry.xml' '/galaxy/server/database/jobs_directory/000/197/upload_params.json' '288:/galaxy/server/database/objects/b/4/4/dataset_b44f93e4-bfca-464d-a379-27ceddc4acca_files:/galaxy/server/database/objects/b/4/4/dataset_b44f93e4-bfca-464d-a379-27ceddc4acca.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_0nlfp5ye\"", + "files_metadata": "{\"__current_case__\": 342, \"file_type\": \"vcf\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"mpileup.X.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_jayzma20\", \"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": "13ba1acd5cd466b0", + "src": "hda", + "uuid": "b44f93e4-bfca-464d-a379-27ceddc4acca" + } + }, + "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-24-09-22-18-15-1/errors/3497a43a628aa539.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/3497a43a628aa539.json new file mode 100644 index 000000000..9b2b6a028 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/3497a43a628aa539.json @@ -0,0 +1,48 @@ +{ + "model_class": "Job", + "id": "3497a43a628aa539", + "history_id": "b2116f9eb07476cf", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0", + "state": "error", + "exit_code": null, + "create_time": "2024-09-22T19:32:02.592388", + "update_time": "2024-09-22T19:32:07.528710", + "galaxy_version": "24.1", + "external_id": "gxy-wfclp", + "handler": null, + "job_runner_name": null, + "command_line": "vcfcreatemulti '/galaxy/server/database/objects/d/9/9/dataset_d99e1928-6dab-496e-8e1b-ba71ca77232c.dat' > '/galaxy/server/database/objects/f/8/2/dataset_f8217004-c37e-4cd0-8d89-f5b32de01fb7.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"vcf\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "break_or_create": "\"create\"" + }, + "inputs": { + "input1": { + "id": "d06e50ccbd12ddff", + "src": "hda", + "uuid": "d99e1928-6dab-496e-8e1b-ba71ca77232c" + } + }, + "outputs": { + "out_file1": { + "id": "ead3b0e6133fe849", + "src": "hda", + "uuid": "f8217004-c37e-4cd0-8d89-f5b32de01fb7" + } + }, + "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-24-09-22-18-15-1/errors/35041e98d94fab80.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/35041e98d94fab80.json new file mode 100644 index 000000000..c9491911a --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/35041e98d94fab80.json @@ -0,0 +1,60 @@ +{ + "model_class": "Job", + "id": "35041e98d94fab80", + "history_id": "b2116f9eb07476cf", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", + "state": "error", + "exit_code": null, + "create_time": "2024-09-22T19:12:07.837952", + "update_time": "2024-09-22T19:12:51.758939", + "galaxy_version": "24.1", + "external_id": "gxy-8zwzq", + "handler": null, + "job_runner_name": null, + "command_line": "mkdir 'tenx.input' && ln -s '/galaxy/server/database/objects/3/f/3/dataset_3f3a1e79-ddd2-4a3b-8a0c-255a2b3dc762.dat' 'tenx.input/matrix.mtx' && ln -s '/galaxy/server/database/objects/f/b/e/dataset_fbe12ec9-a2ac-4d4c-acf6-dc88ad69cfea.dat' 'tenx.input/genes.tsv' && ln -s '/galaxy/server/database/objects/5/1/4/dataset_5147fd90-efd6-45df-8967-a3ae5d8fa9bf.dat' 'tenx.input/barcodes.tsv' && Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/a9caad671439/dropletutils/scripts/dropletutils.Rscript' '/galaxy/server/database/jobs_directory/000/143/configs/tmppyne47_7'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"mtx\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "seed": "\"100\"", + "operation": "{\"__current_case__\": 0, \"method\": {\"__current_case__\": 0, \"expected\": \"3000\", \"lowerprop\": \"0.1\", \"upperquant\": \"0.99\", \"use\": \"defaultdrops\"}, \"outformat\": \"h5\", \"use\": \"filter\"}", + "tenx_format": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 221, \"src\": \"hda\"}]}, \"input_barcodes\": {\"values\": [{\"id\": 223, \"src\": \"hda\"}]}, \"input_genes\": {\"values\": [{\"id\": 222, \"src\": \"hda\"}]}, \"use\": \"directory\"}" + }, + "inputs": { + "tenx_format|input": { + "id": "b8141cadd821f42c", + "src": "hda", + "uuid": "3f3a1e79-ddd2-4a3b-8a0c-255a2b3dc762" + }, + "tenx_format|input_genes": { + "id": "986bd4ea81b0e86b", + "src": "hda", + "uuid": "fbe12ec9-a2ac-4d4c-acf6-dc88ad69cfea" + }, + "tenx_format|input_barcodes": { + "id": "4caf66e9bcb59cbb", + "src": "hda", + "uuid": "5147fd90-efd6-45df-8967-a3ae5d8fa9bf" + } + }, + "outputs": { + "fileout_h5": { + "id": "115df72712751f2b", + "src": "hda", + "uuid": "0d63ccd2-01ba-4bef-a871-82ed36507abc" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 1025\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 1025\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/3a1ae83738ad2097.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/3a1ae83738ad2097.json new file mode 100644 index 000000000..35edba508 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/3a1ae83738ad2097.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "3a1ae83738ad2097", + "history_id": "b2116f9eb07476cf", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-22T19:18:18.442121", + "update_time": "2024-09-22T19:18:32.113800", + "galaxy_version": "24.1", + "external_id": "gxy-7mrp9", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/164/registry.xml' '/galaxy/server/database/jobs_directory/000/164/upload_params.json' '251:/galaxy/server/database/objects/6/5/3/dataset_65383493-7b0c-4fec-8619-3b08c0acb31e_files:/galaxy/server/database/objects/6/5/3/dataset_65383493-7b0c-4fec-8619-3b08c0acb31e.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_1c3mi3iw\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"in_matrix.mtx\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_rqb29y5m\", \"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": "a8832ac7c6c647b7", + "src": "hda", + "uuid": "65383493-7b0c-4fec-8619-3b08c0acb31e" + } + }, + "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-24-09-22-18-15-1/errors/3c44190b9eacecba.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/3c44190b9eacecba.json new file mode 100644 index 000000000..dce4c9f4d --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/3c44190b9eacecba.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "3c44190b9eacecba", + "history_id": "b2116f9eb07476cf", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-22T19:26:01.127709", + "update_time": "2024-09-22T19:26:13.923825", + "galaxy_version": "24.1", + "external_id": "gxy-8rp2r", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/188/registry.xml' '/galaxy/server/database/jobs_directory/000/188/upload_params.json' '279:/galaxy/server/database/objects/8/d/b/dataset_8dbed0ac-d5d0-4501-a8c7-08ec7d986fe9_files:/galaxy/server/database/objects/8/d/b/dataset_8dbed0ac-d5d0-4501-a8c7-08ec7d986fe9.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_wbkakvms\"", + "files_metadata": "{\"__current_case__\": 342, \"file_type\": \"vcf\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"plugin1.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_rz57e17f\", \"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": "de9f71eaa45f3b0d", + "src": "hda", + "uuid": "8dbed0ac-d5d0-4501-a8c7-08ec7d986fe9" + } + }, + "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-24-09-22-18-15-1/errors/536e88f8bbda2931.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/536e88f8bbda2931.json new file mode 100644 index 000000000..d9f2d09d3 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/536e88f8bbda2931.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "536e88f8bbda2931", + "history_id": "b2116f9eb07476cf", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-22T19:28:21.961800", + "update_time": "2024-09-22T19:28:34.583885", + "galaxy_version": "24.1", + "external_id": "gxy-lkd9b", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/198/registry.xml' '/galaxy/server/database/jobs_directory/000/198/upload_params.json' '289:/galaxy/server/database/objects/8/b/e/dataset_8be99a6b-3ef1-480e-b86f-182e2ae6892d_files:/galaxy/server/database/objects/8/b/e/dataset_8be99a6b-3ef1-480e-b86f-182e2ae6892d.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_w16ugrw1\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"mpileup.ploidy\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_9suu1n1k\", \"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": "5782c4c0acf32724", + "src": "hda", + "uuid": "8be99a6b-3ef1-480e-b86f-182e2ae6892d" + } + }, + "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-24-09-22-18-15-1/errors/69d1074d84fd8c41.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/69d1074d84fd8c41.json new file mode 100644 index 000000000..0e82ad5d8 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/69d1074d84fd8c41.json @@ -0,0 +1,60 @@ +{ + "model_class": "Job", + "id": "69d1074d84fd8c41", + "history_id": "b2116f9eb07476cf", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", + "state": "error", + "exit_code": null, + "create_time": "2024-09-22T19:19:02.872642", + "update_time": "2024-09-22T19:19:18.491792", + "galaxy_version": "24.1", + "external_id": "gxy-7svqp", + "handler": null, + "job_runner_name": null, + "command_line": "mkdir 'tenx.input' && ln -s '/galaxy/server/database/objects/f/7/7/dataset_f776d0cb-c106-411c-9e7b-ef6850d588af.dat' 'tenx.input/matrix.mtx' && ln -s '/galaxy/server/database/objects/0/6/f/dataset_06f1f7f5-6ca8-46a7-9ecc-c72ef2db5086.dat' 'tenx.input/genes.tsv' && ln -s '/galaxy/server/database/objects/6/d/4/dataset_6d439c11-4e86-4758-80c5-6d7d9629abd9.dat' 'tenx.input/barcodes.tsv' && Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/a9caad671439/dropletutils/scripts/dropletutils.Rscript' '/galaxy/server/database/jobs_directory/000/170/configs/tmpzm0jjs6k'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"mtx\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "seed": "\"100\"", + "operation": "{\"__current_case__\": 1, \"lower\": \"120\", \"use\": \"barcode_rank\"}", + "tenx_format": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 254, \"src\": \"hda\"}]}, \"input_barcodes\": {\"values\": [{\"id\": 256, \"src\": \"hda\"}]}, \"input_genes\": {\"values\": [{\"id\": 255, \"src\": \"hda\"}]}, \"use\": \"directory\"}" + }, + "inputs": { + "tenx_format|input": { + "id": "fdcac0a8c7aded9e", + "src": "hda", + "uuid": "f776d0cb-c106-411c-9e7b-ef6850d588af" + }, + "tenx_format|input_genes": { + "id": "d822304ea4730230", + "src": "hda", + "uuid": "06f1f7f5-6ca8-46a7-9ecc-c72ef2db5086" + }, + "tenx_format|input_barcodes": { + "id": "dcc8128c9a302db5", + "src": "hda", + "uuid": "6d439c11-4e86-4758-80c5-6d7d9629abd9" + } + }, + "outputs": { + "plot": { + "id": "bbb27daa31c0eea0", + "src": "hda", + "uuid": "eb862c3f-fba6-47c9-8752-78637ce1ee50" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "[1] \"knee = 324 , inflection = 151\"\n", + "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nWarning message:\nIn xy.coords(x, y, xlabel, ylabel, log) :\n 7432 y values <= 0 omitted from logarithmic plot\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "[1] \"knee = 324 , inflection = 151\"\n", + "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nWarning message:\nIn xy.coords(x, y, xlabel, ylabel, log) :\n 7432 y values <= 0 omitted from logarithmic plot\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/6d6283e6a8a1dd61.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/6d6283e6a8a1dd61.json new file mode 100644 index 000000000..f88770e55 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/6d6283e6a8a1dd61.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "6d6283e6a8a1dd61", + "history_id": "b2116f9eb07476cf", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-22T18:49:45.518324", + "update_time": "2024-09-22T18:49:59.364182", + "galaxy_version": "24.1", + "external_id": "gxy-ng9w6", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/54/registry.xml' '/galaxy/server/database/jobs_directory/000/54/upload_params.json' '76:/galaxy/server/database/objects/d/b/7/dataset_db751653-d764-4b56-bd1d-8ffd9dd21dc1_files:/galaxy/server/database/objects/d/b/7/dataset_db751653-d764-4b56-bd1d-8ffd9dd21dc1.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_zsg_a68x\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"test_mapped_reads.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_9h6qxcuz\", \"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": "9114713f5589043b", + "src": "hda", + "uuid": "db751653-d764-4b56-bd1d-8ffd9dd21dc1" + } + }, + "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-24-09-22-18-15-1/errors/79b79e39004a28b8.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/79b79e39004a28b8.json new file mode 100644 index 000000000..d00483fdc --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/79b79e39004a28b8.json @@ -0,0 +1,48 @@ +{ + "model_class": "Job", + "id": "79b79e39004a28b8", + "history_id": "b2116f9eb07476cf", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0", + "state": "error", + "exit_code": null, + "create_time": "2024-09-22T19:31:28.041824", + "update_time": "2024-09-22T19:31:39.111422", + "galaxy_version": "24.1", + "external_id": "gxy-dvw7v", + "handler": null, + "job_runner_name": null, + "command_line": "vcfbreakmulti '/galaxy/server/database/objects/2/e/5/dataset_2e592152-0f70-43bd-bd4d-868b607892ad.dat' > '/galaxy/server/database/objects/d/e/7/dataset_de794ca8-ed39-4aea-94a4-7f51431eb6ab.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"vcf\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "break_or_create": "\"break\"" + }, + "inputs": { + "input1": { + "id": "1dd981024f005b37", + "src": "hda", + "uuid": "2e592152-0f70-43bd-bd4d-868b607892ad" + } + }, + "outputs": { + "out_file1": { + "id": "e28c07939196ceaa", + "src": "hda", + "uuid": "de794ca8-ed39-4aea-94a4-7f51431eb6ab" + } + }, + "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-24-09-22-18-15-1/errors/8341ef21327c738f.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/8341ef21327c738f.json new file mode 100644 index 000000000..8d6e2f4d9 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/8341ef21327c738f.json @@ -0,0 +1,100 @@ +{ + "model_class": "Job", + "id": "8341ef21327c738f", + "history_id": "b2116f9eb07476cf", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1", + "state": "error", + "exit_code": 1, + "create_time": "2024-09-22T18:43:49.771041", + "update_time": "2024-09-22T18:44:29.937202", + "galaxy_version": "24.1", + "external_id": "gxy-dtphr", + "handler": null, + "job_runner_name": null, + "command_line": "poretools events '/galaxy/server/database/objects/3/e/e/dataset_3ee49bdd-4c53-41a8-9007-125f5af29eab.dat' > '/galaxy/server/database/objects/1/a/2/dataset_1a2da447-2fc9-4695-b6f1-b495553b6540.dat'", + "user_email": "tests@fake.org", + "command_version": "", + "params": { + "__input_ext": "\"fast5.tar\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "precalled": "false" + }, + "inputs": { + "input": { + "id": "6449e1892e61ee60", + "src": "hda", + "uuid": "3ee49bdd-4c53-41a8-9007-125f5af29eab" + } + }, + "outputs": { + "output": { + "id": "2911bf8aae422578", + "src": "hda", + "uuid": "1a2da447-2fc9-4695-b6f1-b495553b6540" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/poretools\", line 11, in \n load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 543, in main\n args.func(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 55, in run_subtool\n submodule.run(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/events.py\", line 17, in run\n for fast5 in Fast5File.Fast5FileSet(args.files):\n File \"/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py\", line 110, in next\n shutil.rmtree(PORETOOLS_TMPDIR)\n File \"/usr/local/lib/python2.7/shutil.py\", line 261, in rmtree\n rmtree(fullname, ignore_errors, onerror)\n File \"/usr/local/lib/python2.7/shutil.py\", line 270, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File \"/usr/local/lib/python2.7/shutil.py\", line 268, in rmtree\n os.rmdir(path)\nOSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data'\n", + "job_stdout": "", + "job_stderr": "", + "stdout": "", + "stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/poretools\", line 11, in \n load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 543, in main\n args.func(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 55, in run_subtool\n submodule.run(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/events.py\", line 17, in run\n for fast5 in Fast5File.Fast5FileSet(args.files):\n File \"/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py\", line 110, in next\n shutil.rmtree(PORETOOLS_TMPDIR)\n File \"/usr/local/lib/python2.7/shutil.py\", line 261, in rmtree\n rmtree(fullname, ignore_errors, onerror)\n File \"/usr/local/lib/python2.7/shutil.py\", line 270, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File \"/usr/local/lib/python2.7/shutil.py\", line 268, in rmtree\n os.rmdir(path)\nOSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data'\n", + "job_messages": [ + { + "code_desc": "", + "desc": "Fatal error: Exit code 1 ()", + "error_level": 3, + "exit_code": 1, + "type": "exit_code" + }, + { + "code_desc": "", + "desc": "Fatal error: ", + "error_level": 3, + "match": "Error:", + "stream": "stderr", + "type": "regex" + } + ], + "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": "2024-09-22 18:44:10", + "plugin": "core", + "name": "end_epoch", + "raw_value": "1727030650.0000000" + }, + { + "title": "Job Start Time", + "value": "2024-09-22 18:44:09", + "plugin": "core", + "name": "start_epoch", + "raw_value": "1727030649.0000000" + }, + { + "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" + } + ] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/8964fcf7b6cd4f21.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/8964fcf7b6cd4f21.json new file mode 100644 index 000000000..1ea01db9e --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/8964fcf7b6cd4f21.json @@ -0,0 +1,52 @@ +{ + "model_class": "Job", + "id": "8964fcf7b6cd4f21", + "history_id": "b2116f9eb07476cf", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", + "state": "error", + "exit_code": null, + "create_time": "2024-09-22T19:30:17.021580", + "update_time": "2024-09-22T19:30:22.830517", + "galaxy_version": "24.1", + "external_id": "gxy-qv8pc", + "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/0/8/dataset_c0824522-8e1c-458f-89af-534bd684e8b2.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --group-samples - --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/e/c/1/dataset_ec1837cf-b915-4e32-876c-11435bdbc40d.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "output_type": "\"v\"", + "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": true, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": null, \"skip_variants\": null, \"variants_only\": false}", + "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", + "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 0, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}, \"gvcf\": \"\", \"method\": \"multiallelic\", \"prior\": \"0.0011\", \"prior_freqs\": \"\"}}", + "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}" + }, + "inputs": { + "input_file": { + "id": "ade818caf1f496cb", + "src": "hda", + "uuid": "c0824522-8e1c-458f-89af-534bd684e8b2" + } + }, + "outputs": { + "output_file": { + "id": "850315898bc11a52", + "src": "hda", + "uuid": "ec1837cf-b915-4e32-876c-11435bdbc40d" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/969e5d311cab4b80.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/969e5d311cab4b80.json new file mode 100644 index 000000000..3cb5378f3 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/969e5d311cab4b80.json @@ -0,0 +1,57 @@ +{ + "model_class": "Job", + "id": "969e5d311cab4b80", + "history_id": "b2116f9eb07476cf", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-22T18:36:00.876879", + "update_time": "2024-09-22T18:36:09.259177", + "galaxy_version": "24.1", + "external_id": "gxy-dlhzs", + "handler": null, + "job_runner_name": null, + "command_line": "ln -sf '/galaxy/server/database/objects/9/3/7/dataset_93748e78-babf-44f0-803d-d018408ff776.dat' 'R1_fq.fastq' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for R1_fq.fastq' -i 'R1_fq.fastq' -o first.fastq && mv first.fastq '/galaxy/server/database/objects/4/0/8/dataset_408e1ff7-1252-43ea-8228-26f1b7aeef45.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "output_options": "{\"report_html\": true, \"report_json\": false}", + "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 1, \"poly_g_min_len\": \"\", \"trimming_select\": \"\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": false, \"umi_len\": \"\", \"umi_loc\": null, \"umi_prefix\": null}}", + "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", + "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", + "single_paired": "{\"__current_case__\": 0, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_tail1\": \"\"}, \"in1\": {\"values\": [{\"id\": 10, \"src\": \"hda\"}]}, \"single_paired_selector\": \"single\"}" + }, + "inputs": { + "single_paired|in1": { + "id": "969e5d311cab4b80", + "src": "hda", + "uuid": "93748e78-babf-44f0-803d-d018408ff776" + } + }, + "outputs": { + "out1": { + "id": "674e1020fd2ef73d", + "src": "hda", + "uuid": "408e1ff7-1252-43ea-8228-26f1b7aeef45" + }, + "report_html": { + "id": "91c44c78512c30a5", + "src": "hda", + "uuid": "a3a55db8-8f57-46eb-8f17-72002b84caef" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq \nfastp v0.23.4, time used: 1 seconds\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq \nfastp v0.23.4, time used: 1 seconds\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/d18b8080e14f39b3.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/d18b8080e14f39b3.json new file mode 100644 index 000000000..f9a8b62cb --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/d18b8080e14f39b3.json @@ -0,0 +1,45 @@ +{ + "model_class": "Job", + "id": "d18b8080e14f39b3", + "history_id": "b2116f9eb07476cf", + "tool_id": "upload1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-22T19:19:19.488752", + "update_time": "2024-09-22T19:19:32.188377", + "galaxy_version": "24.1", + "external_id": "gxy-m6s6r", + "handler": null, + "job_runner_name": null, + "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/171/registry.xml' '/galaxy/server/database/jobs_directory/000/171/upload_params.json' '258:/galaxy/server/database/objects/8/3/0/dataset_83017e96-7087-4dff-9e9f-4a25505e69b6_files:/galaxy/server/database/objects/8/3/0/dataset_83017e96-7087-4dff-9e9f-4a25505e69b6.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "paramfile": "\"/galaxy/server/database/tmp/upload_params_0jkjytuh\"", + "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", + "dbkey": "\"?\"", + "force_composite": "\"false\"", + "files": "[{\"NAME\": \"in_matrix.mtx\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_2xnn71io\", \"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": "3f60163d43c904a5", + "src": "hda", + "uuid": "83017e96-7087-4dff-9e9f-4a25505e69b6" + } + }, + "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-24-09-22-18-15-1/errors/d759c259412d2085.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/d759c259412d2085.json new file mode 100644 index 000000000..5e50d4fd0 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/d759c259412d2085.json @@ -0,0 +1,72 @@ +{ + "model_class": "Job", + "id": "d759c259412d2085", + "history_id": "b2116f9eb07476cf", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", + "state": "error", + "exit_code": null, + "create_time": "2024-09-22T18:36:33.485539", + "update_time": "2024-09-22T18:36:39.552742", + "galaxy_version": "24.1", + "external_id": "gxy-d2qls", + "handler": null, + "job_runner_name": null, + "command_line": "ln -sf '/galaxy/server/database/objects/e/6/1/dataset_e61dd1bd-fc1c-471c-bc70-3f5fb7feead8.dat' 'Unnamed Collection.fastq' && ln -sf '/galaxy/server/database/objects/6/7/c/dataset_67cc8ba1-b5bd-4b51-958f-e6178e55d257.dat' 'Unnamed Collection_R2.fastq' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for Unnamed Collection.fastq' -i 'Unnamed Collection.fastq' -o first.fastq -I 'Unnamed Collection_R2.fastq' -O second.fastq && mv first.fastq '/galaxy/server/database/objects/4/c/8/dataset_4c8e8c27-c50b-45f7-aa7e-828119ce7302.dat' && mv second.fastq '/galaxy/server/database/objects/c/d/8/dataset_cd86ba74-decc-4625-8923-ddc02b44fc8d.dat'", + "user_email": "tests@fake.org", + "command_version": null, + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "output_options": "{\"report_html\": true, \"report_json\": false}", + "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 1, \"poly_g_min_len\": \"\", \"trimming_select\": \"\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": false, \"umi_len\": \"\", \"umi_loc\": null, \"umi_prefix\": null}}", + "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", + "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", + "single_paired": "{\"__current_case__\": 2, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"adapter_sequence2\": null, \"detect_adapter_for_pe\": false, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_front2\": \"\", \"trim_tail1\": \"\", \"trim_tail2\": \"\"}, \"paired_input\": {\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}, \"single_paired_selector\": \"paired_collection\"}" + }, + "inputs": { + "single_paired|paired_input1": { + "id": "d759c259412d2085", + "src": "hda", + "uuid": "e61dd1bd-fc1c-471c-bc70-3f5fb7feead8" + }, + "single_paired|paired_input2": { + "id": "681ebc328158e387", + "src": "hda", + "uuid": "67cc8ba1-b5bd-4b51-958f-e6178e55d257" + } + }, + "outputs": { + "output_paired_coll|__part__|forward": { + "id": "10acb56af84768f5", + "src": "hda", + "uuid": "4c8e8c27-c50b-45f7-aa7e-828119ce7302" + }, + "output_paired_coll|__part__|reverse": { + "id": "4db39dbef52fde2f", + "src": "hda", + "uuid": "cd86ba74-decc-4625-8923-ddc02b44fc8d" + }, + "report_html": { + "id": "7adda38f44fa79e6", + "src": "hda", + "uuid": "281df2db-101f-4c40-b836-64c1d2db2cfb" + } + }, + "copied_from_job_id": null, + "output_collections": { + "output_paired_coll": { + "src": "hdca", + "id": "ab630ae25a673765" + } + }, + "tool_stdout": "", + "tool_stderr": "Read1 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 23268(93.6376%)\nQ30 bases: 22391(90.1083%)\n\nRead2 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 22676(91.2552%)\nQ30 bases: 21532(86.6514%)\n\nRead1 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21680(94.4992%)\nQ30 bases: 20981(91.4524%)\n\nRead2 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21535(93.8671%)\nQ30 bases: 20672(90.1055%)\n\nFiltering result:\nreads passed filter: 194\nreads failed due to low quality: 2\nreads failed due to too many N: 2\nreads failed due to too short: 0\nreads with adapter trimmed: 68\nbases trimmed due to adapters: 2824\n\nDuplication rate: 0%\n\nInsert size peak (evaluated by paired-end reads): 308\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for Unnamed Collection.fastq -i Unnamed Collection.fastq -o first.fastq -I Unnamed Collection_R2.fastq -O second.fastq \nfastp v0.23.4, time used: 1 seconds\n", + "job_stdout": null, + "job_stderr": null, + "stdout": "", + "stderr": "Read1 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 23268(93.6376%)\nQ30 bases: 22391(90.1083%)\n\nRead2 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 22676(91.2552%)\nQ30 bases: 21532(86.6514%)\n\nRead1 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21680(94.4992%)\nQ30 bases: 20981(91.4524%)\n\nRead2 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21535(93.8671%)\nQ30 bases: 20672(90.1055%)\n\nFiltering result:\nreads passed filter: 194\nreads failed due to low quality: 2\nreads failed due to too many N: 2\nreads failed due to too short: 0\nreads with adapter trimmed: 68\nbases trimmed due to adapters: 2824\n\nDuplication rate: 0%\n\nInsert size peak (evaluated by paired-end reads): 308\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for Unnamed Collection.fastq -i Unnamed Collection.fastq -o first.fastq -I Unnamed Collection_R2.fastq -O second.fastq \nfastp v0.23.4, time used: 1 seconds\n", + "job_messages": null, + "dependencies": [], + "job_metrics": [] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/dfbed326cfd5efc6.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/dfbed326cfd5efc6.json new file mode 100644 index 000000000..4787d91a9 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/dfbed326cfd5efc6.json @@ -0,0 +1,100 @@ +{ + "model_class": "Job", + "id": "dfbed326cfd5efc6", + "history_id": "b2116f9eb07476cf", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1", + "state": "error", + "exit_code": 1, + "create_time": "2024-09-22T18:44:53.441327", + "update_time": "2024-09-22T18:45:09.790026", + "galaxy_version": "24.1", + "external_id": "gxy-p6hg6", + "handler": null, + "job_runner_name": null, + "command_line": "poretools events --pre-basecalled '/galaxy/server/database/objects/0/6/3/dataset_063614bc-f4dd-4f64-889e-524e4cc70140.dat' > '/galaxy/server/database/objects/f/9/8/dataset_f98ad021-8ef5-40bc-af9d-622b1d5b02ff.dat'", + "user_email": "tests@fake.org", + "command_version": "", + "params": { + "__input_ext": "\"fast5.tar\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "precalled": "true" + }, + "inputs": { + "input": { + "id": "5257353c1238d09b", + "src": "hda", + "uuid": "063614bc-f4dd-4f64-889e-524e4cc70140" + } + }, + "outputs": { + "output": { + "id": "b39a57cfa0641e66", + "src": "hda", + "uuid": "f98ad021-8ef5-40bc-af9d-622b1d5b02ff" + } + }, + "copied_from_job_id": null, + "output_collections": {}, + "tool_stdout": "", + "tool_stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/poretools\", line 11, in \n load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 543, in main\n args.func(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 55, in run_subtool\n submodule.run(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/events.py\", line 13, in run\n for fast5 in Fast5File.Fast5FileSet(args.files):\n File \"/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py\", line 110, in next\n shutil.rmtree(PORETOOLS_TMPDIR)\n File \"/usr/local/lib/python2.7/shutil.py\", line 261, in rmtree\n rmtree(fullname, ignore_errors, onerror)\n File \"/usr/local/lib/python2.7/shutil.py\", line 270, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File \"/usr/local/lib/python2.7/shutil.py\", line 268, in rmtree\n os.rmdir(path)\nOSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data'\n", + "job_stdout": "", + "job_stderr": "", + "stdout": "", + "stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/poretools\", line 11, in \n load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 543, in main\n args.func(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 55, in run_subtool\n submodule.run(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/events.py\", line 13, in run\n for fast5 in Fast5File.Fast5FileSet(args.files):\n File \"/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py\", line 110, in next\n shutil.rmtree(PORETOOLS_TMPDIR)\n File \"/usr/local/lib/python2.7/shutil.py\", line 261, in rmtree\n rmtree(fullname, ignore_errors, onerror)\n File \"/usr/local/lib/python2.7/shutil.py\", line 270, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File \"/usr/local/lib/python2.7/shutil.py\", line 268, in rmtree\n os.rmdir(path)\nOSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data'\n", + "job_messages": [ + { + "code_desc": "", + "desc": "Fatal error: Exit code 1 ()", + "error_level": 3, + "exit_code": 1, + "type": "exit_code" + }, + { + "code_desc": "", + "desc": "Fatal error: ", + "error_level": 3, + "match": "Error:", + "stream": "stderr", + "type": "regex" + } + ], + "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": "2024-09-22 18:44:56", + "plugin": "core", + "name": "end_epoch", + "raw_value": "1727030696.0000000" + }, + { + "title": "Job Start Time", + "value": "2024-09-22 18:44:55", + "plugin": "core", + "name": "start_epoch", + "raw_value": "1727030695.0000000" + }, + { + "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" + } + ] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/f460fb6ee726512e.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/f460fb6ee726512e.json new file mode 100644 index 000000000..c7afa2827 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/errors/f460fb6ee726512e.json @@ -0,0 +1,116 @@ +{ + "model_class": "Job", + "id": "f460fb6ee726512e", + "history_id": "b2116f9eb07476cf", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", + "state": "error", + "exit_code": 255, + "create_time": "2024-09-22T18:43:07.768195", + "update_time": "2024-09-22T18:43:22.893312", + "galaxy_version": "24.1", + "external_id": "gxy-767g9", + "handler": null, + "job_runner_name": null, + "command_line": "ln -sf '/galaxy/server/database/objects/c/6/d/dataset_c6df2c59-d07b-4247-b6cf-0f52c8818ca9.dat' 'Unnamed Collection.fastq' && ln -sf '/galaxy/server/database/objects/7/2/0/dataset_72074a2f-62f9-45ff-b5e7-ab01d0cb2c3b.dat' 'Unnamed Collection_R2.fastq' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for Unnamed Collection.fastq' -i 'Unnamed Collection.fastq' -o first.fastq -I 'Unnamed Collection_R2.fastq' -O second.fastq && mv first.fastq '/galaxy/server/database/objects/8/d/8/dataset_8d80d5b6-a9d8-42f4-b9ea-5e1095e22e1c.dat' && mv second.fastq '/galaxy/server/database/objects/c/e/5/dataset_ce5560a4-4b37-4703-a8eb-e11d117ffe0b.dat'", + "user_email": "tests@fake.org", + "command_version": "fastp 0.23.4", + "params": { + "__input_ext": "\"input\"", + "dbkey": "\"?\"", + "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", + "output_options": "{\"report_html\": true, \"report_json\": false}", + "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 1, \"poly_g_min_len\": \"\", \"trimming_select\": \"\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": false, \"umi_len\": \"\", \"umi_loc\": null, \"umi_prefix\": null}}", + "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", + "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", + "single_paired": "{\"__current_case__\": 2, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"adapter_sequence2\": null, \"detect_adapter_for_pe\": false, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_front2\": \"\", \"trim_tail1\": \"\", \"trim_tail2\": \"\"}, \"paired_input\": {\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}, \"single_paired_selector\": \"paired_collection\"}" + }, + "inputs": { + "single_paired|paired_input1": { + "id": "0c0369322ab0183a", + "src": "hda", + "uuid": "c6df2c59-d07b-4247-b6cf-0f52c8818ca9" + }, + "single_paired|paired_input2": { + "id": "df041e0a5e2a496e", + "src": "hda", + "uuid": "72074a2f-62f9-45ff-b5e7-ab01d0cb2c3b" + } + }, + "outputs": { + "output_paired_coll|__part__|forward": { + "id": "ce67f983aab93dca", + "src": "hda", + "uuid": "8d80d5b6-a9d8-42f4-b9ea-5e1095e22e1c" + }, + "output_paired_coll|__part__|reverse": { + "id": "6d6283e6a8a1dd61", + "src": "hda", + "uuid": "ce5560a4-4b37-4703-a8eb-e11d117ffe0b" + }, + "report_html": { + "id": "57b30d8abe5104ed", + "src": "hda", + "uuid": "657721a4-9a11-4b8b-820c-74c731ee44a2" + } + }, + "copied_from_job_id": null, + "output_collections": { + "output_paired_coll": { + "src": "hdca", + "id": "22bd9d5c76a71522" + } + }, + "tool_stdout": "", + "tool_stderr": "\nWARNNIG: different read numbers of the 0 pack\nRead1 pack size: 99\nRead2 pack size: 100\n\nERROR: input files don't contain identical amount of reads\n", + "job_stdout": "", + "job_stderr": "", + "stdout": "", + "stderr": "\nWARNNIG: different read numbers of the 0 pack\nRead1 pack size: 99\nRead2 pack size: 100\n\nERROR: input files don't contain identical amount of reads\n", + "job_messages": [ + { + "code_desc": "", + "desc": "Fatal error: Exit code 255 ()", + "error_level": 3, + "exit_code": 255, + "type": "exit_code" + } + ], + "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": "2024-09-22 18:43:10", + "plugin": "core", + "name": "end_epoch", + "raw_value": "1727030590.0000000" + }, + { + "title": "Job Start Time", + "value": "2024-09-22 18:43:09", + "plugin": "core", + "name": "start_epoch", + "raw_value": "1727030589.0000000" + }, + { + "title": "Memory Allocated (MB)", + "value": "16320", + "plugin": "core", + "name": "galaxy_memory_mb", + "raw_value": "16320.0000000" + }, + { + "title": "Cores Allocated", + "value": "4", + "plugin": "core", + "name": "galaxy_slots", + "raw_value": "4.0000000" + } + ] +} diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/job-metrics.csv b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/job-metrics.csv new file mode 100644 index 000000000..5ffd843f2 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/job-metrics.csv @@ -0,0 +1,215 @@ 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+b2116f9eb07476cf,b2116f9eb07476cf,anvil-test-2024-09-22-18-31,ok,upload1,,,,4080.0000000,1.0000000,,,,,,8.0000000 diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/jobs.txt b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/jobs.txt new file mode 100644 index 000000000..f17e0cf74 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/jobs.txt @@ -0,0 +1,214 @@ +55702ef40a7a761e ok 2024-09-22T19:32:46.685505 toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc3+galaxy0 +3f96f37bdde89dc8 ok 2024-09-22T19:32:31.348122 upload1 +3497a43a628aa539 error 2024-09-22T19:32:07.528710 toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0 +e0b6f6a52350c93e ok 2024-09-22T19:32:02.244361 upload1 +79b79e39004a28b8 error 2024-09-22T19:31:39.111422 toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc3+galaxy0 +287e2b63bf1cda5c ok 2024-09-22T19:31:27.730621 upload1 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toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5 +08129bff60830b9f ok 2024-09-22T19:28:04.146454 upload1 +a6fe0632b4051f26 ok 2024-09-22T19:28:03.420043 upload1 +4a4c437003421748 ok 2024-09-22T19:28:02.317732 upload1 +3ae329f523d924dd ok 2024-09-22T19:27:34.476800 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5 +086d8c7a975b8162 ok 2024-09-22T19:27:18.391610 upload1 +f961682aef856eb4 ok 2024-09-22T19:26:54.933431 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5 +31c5463959644015 ok 2024-09-22T19:26:39.080826 upload1 +3c44190b9eacecba error 2024-09-22T19:26:13.923825 upload1 +672228a56bae35c2 ok 2024-09-22T19:26:00.185269 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_setgt/bcftools_plugin_setgt/1.15.1+galaxy4 +c5b5d01ee754942c ok 2024-09-22T19:25:40.008073 upload1 +18ce24bae044c619 ok 2024-09-22T19:25:09.985323 toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0 +3b8192f8a065be0a ok 2024-09-22T19:24:42.608057 upload1 +e4fe8429e6deaecc ok 2024-09-22T19:24:20.356301 toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0 +6292de7301fba0eb ok 2024-09-22T19:23:53.024043 upload1 +412f6bf3e98cc878 ok 2024-09-22T19:23:30.217522 toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0 +fe33575f0500b13e ok 2024-09-22T19:23:01.449389 upload1 +1280ceb1907d7cfb ok 2024-09-22T19:22:38.190717 toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0 +a28a75871b82f3c6 ok 2024-09-22T19:21:42.276829 upload1 +1ac46435ea78d248 ok 2024-09-22T19:21:17.640981 toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 +311c79364e89d97c ok 2024-09-22T19:20:51.282738 upload1 +2f925a76a0742f8a ok 2024-09-22T19:20:25.989737 toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 +a8b2ceb9efb9e894 ok 2024-09-22T19:19:55.205649 upload1 +5595cb07e7491dd7 ok 2024-09-22T19:19:44.768995 upload1 +90d0613a52964397 ok 2024-09-22T19:19:43.610126 upload1 +d18b8080e14f39b3 error 2024-09-22T19:19:32.188377 upload1 +69d1074d84fd8c41 error 2024-09-22T19:19:18.491792 toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 +c930c740de7e1125 ok 2024-09-22T19:19:02.543352 upload1 +880a1ea5956edb18 ok 2024-09-22T19:19:02.407167 upload1 +053bd85423bed0e1 ok 2024-09-22T19:19:02.236215 upload1 +6978290ff24c69ad ok 2024-09-22T19:18:43.256607 upload1 +3a25d7a20db9a9e7 ok 2024-09-22T19:18:43.205821 upload1 +3a1ae83738ad2097 error 2024-09-22T19:18:32.113800 upload1 +916cf8497eadecb5 ok 2024-09-22T19:18:17.272123 toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 +48399b7ba6094602 ok 2024-09-22T19:17:52.065903 upload1 +43cc8889bf9e8f95 ok 2024-09-22T19:17:51.920855 upload1 +f39f4c30dcd74940 ok 2024-09-22T19:17:50.905372 upload1 +400fd7205f084227 ok 2024-09-22T19:17:20.296017 toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 +cd988844606043bf ok 2024-09-22T19:16:54.078510 upload1 +00bf5e33f5f60a84 error 2024-09-22T19:16:29.622402 toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 +5fc19491eaefd6a0 ok 2024-09-22T19:16:09.103524 upload1 +02f38e9397fe15a2 ok 2024-09-22T19:15:43.944528 toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 +16aec2a9adba5ff8 ok 2024-09-22T19:15:16.571045 upload1 +b46e8f57ace2c24f ok 2024-09-22T19:15:16.307580 upload1 +9cb5d6626b0ce3fb ok 2024-09-22T19:15:14.881931 upload1 +0b1249106278121c ok 2024-09-22T19:14:45.897612 toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 +5f43fff7662f5bd9 ok 2024-09-22T19:14:19.450802 upload1 +e1e933b2ae1e5064 ok 2024-09-22T19:14:19.410041 upload1 +5293f70d910a91cb ok 2024-09-22T19:14:19.402502 upload1 +02aa1fe4b4b7ee2b ok 2024-09-22T19:13:47.874183 toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 +f8c32272d7e25d25 ok 2024-09-22T19:13:22.609479 upload1 +5846fbfc8b245451 ok 2024-09-22T19:13:21.826329 upload1 +d285955c2fd14290 ok 2024-09-22T19:13:21.531401 upload1 +35041e98d94fab80 error 2024-09-22T19:12:51.758939 toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 +5f3de9ec851a1bbe ok 2024-09-22T19:12:07.548849 upload1 +7cf6ffdc5f6c3d4a ok 2024-09-22T19:12:07.501141 upload1 +fc3d9705f1d58da1 ok 2024-09-22T19:12:07.428901 upload1 +232511db0762de5b ok 2024-09-22T19:11:34.686958 toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 +24371a49dc8408da ok 2024-09-22T19:11:19.270735 upload1 +6409a12dbea93ff2 ok 2024-09-22T19:11:19.182389 upload1 +6fab46106d565c01 ok 2024-09-22T19:10:54.246758 toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 +38f756a732f89588 ok 2024-09-22T19:10:38.705477 upload1 +50cb20a192d153eb ok 2024-09-22T19:10:37.859440 upload1 +68822d38a18be506 ok 2024-09-22T19:10:13.896898 toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 +8e3cd42fade67d71 ok 2024-09-22T19:09:57.970995 upload1 +87f1dec4b968275c ok 2024-09-22T19:09:57.086853 upload1 +67f4878618a03e81 ok 2024-09-22T19:09:32.901110 toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 +c7c9bd45055a66e2 ok 2024-09-22T19:09:16.397634 upload1 +f1ba1165aac2478e ok 2024-09-22T19:09:15.148391 upload1 +a627cd48f111ee3e ok 2024-09-22T19:08:51.586694 toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 +e8b7c9916a5502ab ok 2024-09-22T19:08:35.907834 upload1 +2659c783a61b04b5 ok 2024-09-22T19:08:35.042312 upload1 +13cdcdbe98abef25 ok 2024-09-22T19:08:09.850141 toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 +6e5355263cf67873 ok 2024-09-22T19:07:54.479486 upload1 +228875ce427a57fd ok 2024-09-22T19:07:54.420915 upload1 +31ba71a5468dd219 ok 2024-09-22T19:07:29.072922 toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 +a0d815711ed73e82 ok 2024-09-22T19:07:13.084987 upload1 +1e1b7bbb50087229 ok 2024-09-22T19:06:48.710240 toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 +257a1458dc621405 ok 2024-09-22T19:06:33.193688 upload1 +3893451f16a76961 ok 2024-09-22T19:06:32.279583 upload1 +7caf0227b06d2b6d ok 2024-09-22T19:06:08.093569 toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 +711d1c6a832e4812 ok 2024-09-22T19:05:52.189221 upload1 +92e4a16636f870a1 ok 2024-09-22T19:05:28.820893 toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 +73bce02258136c59 ok 2024-09-22T19:05:12.552186 upload1 +755753a41550366c ok 2024-09-22T19:05:12.535612 upload1 +0b2bd508b8904d58 ok 2024-09-22T19:04:47.408813 toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 +e4ac1ace7cb0990a ok 2024-09-22T19:04:31.756416 upload1 +0261da2dfe29a82a ok 2024-09-22T19:04:30.863417 upload1 +cee84bce56029b58 ok 2024-09-22T19:04:06.718068 toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 +24755ecc2498cdfd ok 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b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/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-24-09-22-18-15-1/results.json b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/results.json new file mode 100644 index 000000000..6cb0480da --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/results.json @@ -0,0 +1 @@ +{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 90, "errors": 12, "failures": 10, "skips": 0}, "tests": [{"id": "bcftools_call/1.15.1+galaxy5-0", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 0, "time_seconds": 40.487770318984985, "inputs": {"input_file": {"src": "hda", "id": "7b5d219aa87789ca"}, "sec_consensus_variant_calling|variant_calling|method": "multiallelic", "sec_input_output|variants_only": true, "output_type": "v"}, "job": {"model_class": "Job", "id": "f961682aef856eb4", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:26:39.378050", "update_time": "2024-09-22T19:26:54.933431", "galaxy_version": "24.1", "external_id": "gxy-fl9wc", "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/6/dataset_ec676054-0d89-4b73-8ee3-ef8f371d8d07.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --variants-only --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/c/6/d/dataset_c6df096c-f43b-45c4-96ce-ab99338449d3.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": false, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": null, \"skip_variants\": null, \"variants_only\": true}", "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 0, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}, \"gvcf\": \"\", \"method\": \"multiallelic\", \"prior\": \"0.0011\", \"prior_freqs\": \"\"}}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}"}, "inputs": {"input_file": {"id": "7b5d219aa87789ca", "src": "hda", "uuid": "ec676054-0d89-4b73-8ee3-ef8f371d8d07"}}, "outputs": {"output_file": {"id": "22fb54ab6570d8b8", "src": "hda", "uuid": "c6df096c-f43b-45c4-96ce-ab99338449d3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\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": "2024-09-22 19:26:41", "plugin": "core", "name": "end_epoch", "raw_value": "1727033201.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:26:41", "plugin": "core", "name": "start_epoch", "raw_value": "1727033201.0000000"}, {"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_call/1.15.1+galaxy5-1", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 1, "time_seconds": 39.37793803215027, "inputs": {"input_file": {"src": "hda", "id": "1b0f7661249012e4"}, "sec_consensus_variant_calling|variant_calling|gvcf": "0", "sec_consensus_variant_calling|variant_calling|method": "multiallelic", "output_type": "v"}, "job": {"model_class": "Job", "id": "3ae329f523d924dd", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:27:18.556626", "update_time": "2024-09-22T19:27:34.476800", "galaxy_version": "24.1", "external_id": "gxy-879fq", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/4/0/a/dataset_40aa0b30-1c8f-4bcb-b414-32fc0a49ed63.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --gvcf 0 --prior 0.0011 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/2/2/4/dataset_22475985-a067-4d48-bb97-73e0bc50de21.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": false, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": null, \"skip_variants\": null, \"variants_only\": false}", "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 0, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}, \"gvcf\": \"0\", \"method\": \"multiallelic\", \"prior\": \"0.0011\", \"prior_freqs\": \"\"}}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}"}, "inputs": {"input_file": {"id": "1b0f7661249012e4", "src": "hda", "uuid": "40aa0b30-1c8f-4bcb-b414-32fc0a49ed63"}}, "outputs": {"output_file": {"id": "6daa875bd2d70d64", "src": "hda", "uuid": "22475985-a067-4d48-bb97-73e0bc50de21"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\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": "2024-09-22 19:27:20", "plugin": "core", "name": "end_epoch", "raw_value": "1727033240.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:27:20", "plugin": "core", "name": "start_epoch", "raw_value": "1727033240.0000000"}, {"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_call/1.15.1+galaxy5-2", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 2, "time_seconds": 46.18582344055176, "inputs": {"input_file": {"src": "hda", "id": "49aa8e2b8dffb426"}, "sec_restrict|samples_file": {"src": "hda", "id": "fcc22db9cd39eaf4"}, "sec_consensus_variant_calling|variant_calling|method": "multiallelic", "sec_file_format|ploidy_file": {"src": "hda", "id": "d6f69d10cc573f39"}, "output_type": "v"}, "job": {"model_class": "Job", "id": "4df9a0e9bf061626", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:28:04.361163", "update_time": "2024-09-22T19:28:20.719532", "galaxy_version": "24.1", "external_id": "gxy-pm7dl", "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/e/7/dataset_ee769dc2-0f1c-4818-b9bd-d1325ee64f21.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --samples-file \"/galaxy/server/database/objects/c/1/1/dataset_c1168e82-4b0f-4351-841b-98688847897c.dat\" --ploidy-file '/galaxy/server/database/objects/9/d/3/dataset_9d3f1ce8-64f3-4221-a301-615972352b5d.dat' --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/2/a/2/dataset_2a278a8a-33a9-4597-91db-af14efdb2755.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": false, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": null, \"skip_variants\": null, \"variants_only\": false}", "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": {\"values\": [{\"id\": 286, \"src\": \"hda\"}]}, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 0, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}, \"gvcf\": \"\", \"method\": \"multiallelic\", \"prior\": \"0.0011\", \"prior_freqs\": \"\"}}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": {\"values\": [{\"id\": 285, \"src\": \"hda\"}]}}"}, "inputs": {"input_file": {"id": "49aa8e2b8dffb426", "src": "hda", "uuid": "ee769dc2-0f1c-4818-b9bd-d1325ee64f21"}, "sec_restrict|samples_file": {"id": "fcc22db9cd39eaf4", "src": "hda", "uuid": "c1168e82-4b0f-4351-841b-98688847897c"}, "sec_file_format|ploidy_file": {"id": "d6f69d10cc573f39", "src": "hda", "uuid": "9d3f1ce8-64f3-4221-a301-615972352b5d"}}, "outputs": {"output_file": {"id": "03b118dc08aa9689", "src": "hda", "uuid": "2a278a8a-33a9-4597-91db-af14efdb2755"}}, "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": "2024-09-22 19:28:06", "plugin": "core", "name": "end_epoch", "raw_value": "1727033286.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:28:06", "plugin": "core", "name": "start_epoch", "raw_value": "1727033286.0000000"}, {"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_call/1.15.1+galaxy5-3", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 3, "time_seconds": 13.378509759902954, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bcftools_call/1.15.1+galaxy5-4", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 4, "time_seconds": 39.97740602493286, "inputs": {"input_file": {"src": "hda", "id": "7dd87a216ecf1e00"}, "sec_consensus_variant_calling|variant_calling|method": "consensus", "sec_file_format|ploidy_file": {"src": "hda", "id": "b26dd42d38fb43b0"}, "sec_input_output|output_tags": "INFO/PV4", "output_type": "v"}, "job": {"model_class": "Job", "id": "c54c8af4d191f7fb", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:28:58.746996", "update_time": "2024-09-22T19:29:13.925094", "galaxy_version": "24.1", "external_id": "gxy-r7ljg", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/b/e/dataset_fbe6acea-152e-48c3-85d5-ae22c7a6d7b0.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -c --pval-threshold 0.5 --ploidy-file '/galaxy/server/database/objects/1/a/7/dataset_1a705e40-10e9-419f-b3fc-0b66d7ac537a.dat' --annotate INFO/PV4 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/1/a/4/dataset_1a4d8113-5594-478b-bab8-8719155876ae.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": false, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": \"INFO/PV4\", \"skip_variants\": null, \"variants_only\": false}", "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": {\"values\": [{\"id\": 291, \"src\": \"hda\"}]}, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 1, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\"}, \"method\": \"consensus\", \"pval_threshold\": \"0.5\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}"}, "inputs": {"input_file": {"id": "7dd87a216ecf1e00", "src": "hda", "uuid": "fbe6acea-152e-48c3-85d5-ae22c7a6d7b0"}, "sec_file_format|ploidy_file": {"id": "b26dd42d38fb43b0", "src": "hda", "uuid": "1a705e40-10e9-419f-b3fc-0b66d7ac537a"}}, "outputs": {"output_file": {"id": "defc28b43480aac5", "src": "hda", "uuid": "1a4d8113-5594-478b-bab8-8719155876ae"}}, "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": "2024-09-22 19:29:00", "plugin": "core", "name": "end_epoch", "raw_value": "1727033340.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:29:00", "plugin": "core", "name": "start_epoch", "raw_value": "1727033340.0000000"}, {"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_call/1.15.1+galaxy5-5", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 5, "time_seconds": 38.90674376487732, "inputs": {"input_file": {"src": "hda", "id": "c5f1e267961fefaf"}, "sec_restrict|regions_overlap": "1", "sec_consensus_variant_calling|variant_calling|method": "multiallelic", "sec_input_output|variants_only": true, "output_type": "v"}, "job": {"model_class": "Job", "id": "66af1366e0051fb7", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:29:37.483989", "update_time": "2024-09-22T19:29:53.024921", "galaxy_version": "24.1", "external_id": "gxy-5mhjf", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/1/5/4/dataset_154d85bc-1823-4c7f-9f74-a2b81d49a632.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --regions-overlap 1 --variants-only --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/5/f/7/dataset_5f72c8a8-42d3-42d9-a7d8-312a87bba4e5.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": false, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": null, \"skip_variants\": null, \"variants_only\": true}", "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 0, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}, \"gvcf\": \"\", \"method\": \"multiallelic\", \"prior\": \"0.0011\", \"prior_freqs\": \"\"}}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": \"1\", \"samples\": \"\", \"samples_file\": null}"}, "inputs": {"input_file": {"id": "c5f1e267961fefaf", "src": "hda", "uuid": "154d85bc-1823-4c7f-9f74-a2b81d49a632"}}, "outputs": {"output_file": {"id": "5238f4162da7f1cf", "src": "hda", "uuid": "5f72c8a8-42d3-42d9-a7d8-312a87bba4e5"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\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": "2024-09-22 19:29:39", "plugin": "core", "name": "end_epoch", "raw_value": "1727033379.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:29:39", "plugin": "core", "name": "start_epoch", "raw_value": "1727033379.0000000"}, {"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_call/1.15.1+galaxy5-6", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 6, "time_seconds": 29.62593984603882, "inputs": {"input_file": {"src": "hda", "id": "ade818caf1f496cb"}, "sec_consensus_variant_calling|variant_calling|method": "multiallelic", "sec_input_output|group_samples": true, "output_type": "v"}, "job": {"model_class": "Job", "id": "8964fcf7b6cd4f21", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "state": "error", "exit_code": null, "create_time": "2024-09-22T19:30:17.021580", "update_time": "2024-09-22T19:30:22.830517", "galaxy_version": "24.1", "external_id": "gxy-qv8pc", "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/0/8/dataset_c0824522-8e1c-458f-89af-534bd684e8b2.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --group-samples - --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/e/c/1/dataset_ec1837cf-b915-4e32-876c-11435bdbc40d.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": true, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": null, \"skip_variants\": null, \"variants_only\": false}", "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 0, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\", \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}, \"gvcf\": \"\", \"method\": \"multiallelic\", \"prior\": \"0.0011\", \"prior_freqs\": \"\"}}", "sec_restrict": "{\"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}"}, "inputs": {"input_file": {"id": "ade818caf1f496cb", "src": "hda", "uuid": "c0824522-8e1c-458f-89af-534bd684e8b2"}}, "outputs": {"output_file": {"id": "850315898bc11a52", "src": "hda", "uuid": "ec1837cf-b915-4e32-876c-11435bdbc40d"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, exit_code: None, stderr: Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5, exit_code: None, stderr: Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n."], "status": "failure"}}, {"id": "bcftools_call/1.15.1+galaxy5-7", "has_data": true, "data": {"tool_id": "bcftools_call", "tool_version": "1.15.1+galaxy5", "test_index": 7, "time_seconds": 40.76142692565918, "inputs": {"input_file": {"src": "hda", "id": "aea75c85b4fb4b67"}, "sec_consensus_variant_calling|variant_calling|genotypes|targets|targets_file": {"src": "hda", "id": "d3de7c9db7d42992"}, "sec_consensus_variant_calling|variant_calling|genotypes|targets|targets_src": "targets_file", "sec_consensus_variant_calling|variant_calling|method": "multiallelic", "output_type": "v"}, "job": {"model_class": "Job", "id": "8a49f506703cd689", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:30:47.596321", "update_time": "2024-09-22T19:31:03.585806", "galaxy_version": "24.1", "external_id": "gxy-zvfj4", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/5/f/f/dataset_5ff2a26f-d1d0-4202-b3d8-8f07f542dcdd.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools call -m --prior 0.0011 --targets-file \"/galaxy/server/database/objects/5/8/9/dataset_589c04ba-2957-4afd-8dca-cca29e381faa.dat\" --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/galaxy/server/database/objects/e/7/0/dataset_e704aa19-d4a4-4e1a-b5a7-fe46496c0f01.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.15.1 (using htslib 1.15.1)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "sec_input_output": "{\"format_fields\": \"\", \"group_samples\": false, \"keep_alts\": false, \"keep_masked_ref\": false, \"output_tags\": null, \"skip_variants\": null, \"variants_only\": false}", "sec_file_format": "{\"invert_samples\": false, \"invert_samples_file\": false, \"ploidy\": null, \"ploidy_file\": null, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": null, \"samples\": \"\", \"samples_file\": null}", "sec_consensus_variant_calling": "{\"variant_calling\": {\"__current_case__\": 0, \"genotypes\": {\"__current_case__\": 0, \"constrain\": \"none\", \"targets\": {\"__current_case__\": 2, \"invert_targets_file\": false, \"targets_file\": {\"values\": [{\"id\": 298, \"src\": \"hda\"}]}, \"targets_src\": \"targets_file\"}, \"targets_overlap\": null}, \"gvcf\": \"\", \"method\": \"multiallelic\", \"prior\": \"0.0011\", \"prior_freqs\": \"\"}}", 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"{\"__current_case__\": 0, \"method\": {\"__current_case__\": 0, \"expected\": \"3000\", \"lowerprop\": \"0.1\", \"upperquant\": \"0.99\", \"use\": \"defaultdrops\"}, \"outformat\": \"h5\", \"use\": \"filter\"}", "tenx_format": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 221, \"src\": \"hda\"}]}, \"input_barcodes\": {\"values\": [{\"id\": 223, \"src\": \"hda\"}]}, \"input_genes\": {\"values\": [{\"id\": 222, \"src\": \"hda\"}]}, \"use\": \"directory\"}"}, "inputs": {"tenx_format|input": {"id": "b8141cadd821f42c", "src": "hda", "uuid": "3f3a1e79-ddd2-4a3b-8a0c-255a2b3dc762"}, "tenx_format|input_genes": {"id": "986bd4ea81b0e86b", "src": "hda", "uuid": "fbe12ec9-a2ac-4d4c-acf6-dc88ad69cfea"}, "tenx_format|input_barcodes": {"id": "4caf66e9bcb59cbb", "src": "hda", "uuid": "5147fd90-efd6-45df-8967-a3ae5d8fa9bf"}}, "outputs": {"fileout_h5": {"id": "115df72712751f2b", "src": "hda", "uuid": "0d63ccd2-01ba-4bef-a871-82ed36507abc"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 1025\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 1025\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, exit_code: None, stderr: Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 1025\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, exit_code: None, stderr: Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 1025\n."], "status": "failure"}}, {"id": "dropletutils/1.10.0+galaxy2-0", "has_data": true, "data": {"tool_id": "dropletutils", "tool_version": "1.10.0+galaxy2", "test_index": 0, "time_seconds": 55.27091860771179, "inputs": {"tenx_format|input": {"src": "hda", "id": "ad95bdae3ab0b239"}, "tenx_format|input_genes": {"src": "hda", "id": "8d99b2bd45f70b36"}, "tenx_format|input_barcodes": {"src": "hda", "id": "4ee1aec9a43cda1c"}, "tenx_format|use": "directory", "operation|outformat": "h5", "operation|use": "filter"}, "job": {"model_class": "Job", "id": "916cf8497eadecb5", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:17:52.382676", "update_time": "2024-09-22T19:18:17.272123", "galaxy_version": "24.1", "external_id": "gxy-mznb2", "handler": null, "job_runner_name": null, "command_line": "mkdir 'tenx.input' && ln -s '/galaxy/server/database/objects/4/1/8/dataset_418d1c71-00bf-406e-9e2d-e63f172660f9.dat' 'tenx.input/matrix.mtx' && ln -s '/galaxy/server/database/objects/b/2/9/dataset_b293b491-54e5-45e1-8ef9-5bd63d218223.dat' 'tenx.input/genes.tsv' && ln -s '/galaxy/server/database/objects/0/8/c/dataset_08ce4bd9-f921-41c2-a6dc-00b3319ddf8e.dat' 'tenx.input/barcodes.tsv' && Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/a9caad671439/dropletutils/scripts/dropletutils.Rscript' '/galaxy/server/database/jobs_directory/000/163/configs/tmpcmkwubdb'", "user_email": "tests@fake.org", "command_version": "grep: invalid option -- 'P'\nBusyBox v1.22.1 (2014-05-23 01:24:27 UTC) multi-call binary.\n\nUsage: grep [-HhnlLoqvsriwFE] [-m N] [-A/B/C N] PATTERN/-e PATTERN.../-f FILE [FILE]...\n\nSearch for PATTERN in FILEs (or stdin)\n\n\t-H\tAdd 'filename:' prefix\n\t-h\tDo not add 'filename:' prefix\n\t-n\tAdd 'line_no:' prefix\n\t-l\tShow only names of files that match\n\t-L\tShow only names of files that don't match\n\t-c\tShow only count of matching lines\n\t-o\tShow only the matching part of line\n\t-q\tQuiet. Return 0 if PATTERN is found, 1 otherwise\n\t-v\tSelect non-matching lines\n\t-s\tSuppress open and read errors\n\t-r\tRecurse\n\t-i\tIgnore case\n\t-w\tMatch whole words only\n\t-x\tMatch whole lines only\n\t-F\tPATTERN is a literal (not regexp)\n\t-E\tPATTERN is an extended regexp\n\t-m N\tMatch up to N times per file\n\t-A N\tPrint N lines of trailing context\n\t-B N\tPrint N lines of leading context\n\t-C N\tSame as '-A N -B N'\n\t-e PTRN\tPattern to match\n\t-f FILE\tRead pattern from file", "params": {"__input_ext": "\"mtx\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"100\"", "operation": "{\"__current_case__\": 0, \"method\": {\"__current_case__\": 0, \"expected\": \"3000\", \"lowerprop\": \"0.1\", \"upperquant\": \"0.99\", \"use\": \"defaultdrops\"}, \"outformat\": \"h5\", \"use\": \"filter\"}", "tenx_format": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 247, \"src\": \"hda\"}]}, \"input_barcodes\": {\"values\": [{\"id\": 249, \"src\": \"hda\"}]}, \"input_genes\": {\"values\": [{\"id\": 248, \"src\": \"hda\"}]}, \"use\": \"directory\"}"}, "inputs": {"tenx_format|input": {"id": "ad95bdae3ab0b239", "src": "hda", "uuid": "418d1c71-00bf-406e-9e2d-e63f172660f9"}, "tenx_format|input_genes": {"id": "8d99b2bd45f70b36", "src": "hda", "uuid": "b293b491-54e5-45e1-8ef9-5bd63d218223"}, "tenx_format|input_barcodes": {"id": "4ee1aec9a43cda1c", "src": "hda", "uuid": "08ce4bd9-f921-41c2-a6dc-00b3319ddf8e"}}, "outputs": {"fileout_h5": {"id": "abb569dec4583ed7", "src": "hda", "uuid": "026e885d-73fa-4c4b-93cc-7e4ea78aa7d1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 1025\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 1025\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "11 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "11.0000000"}, {"title": "Job End Time", "value": "2024-09-22 19:18:04", "plugin": "core", "name": "end_epoch", "raw_value": "1727032684.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:17:53", "plugin": "core", "name": "start_epoch", "raw_value": "1727032673.0000000"}, {"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": "dropletutils/1.10.0+galaxy2-1", "has_data": true, "data": {"tool_id": "dropletutils", "tool_version": "1.10.0+galaxy2", "test_index": 1, "time_seconds": 56.24971270561218, "inputs": {"tenx_format|input": {"src": "hda", "id": "ccee83cbcfb78bc9"}, "tenx_format|input_genes": {"src": "hda", "id": "ff87f8ffbc7820f9"}, "tenx_format|input_barcodes": {"src": "hda", "id": "d85a18590724a5b8"}, "tenx_format|use": "directory", "operation|outformat": "tsv", "operation|use": "filter"}, "job": {"model_class": "Job", "id": "02aa1fe4b4b7ee2b", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:13:23.019124", "update_time": "2024-09-22T19:13:47.874183", "galaxy_version": "24.1", "external_id": "gxy-5xdrx", "handler": null, "job_runner_name": null, "command_line": "mkdir 'tenx.input' && ln -s '/galaxy/server/database/objects/7/e/6/dataset_7e61ecaf-fa41-4a24-aa5c-dc3d9c4c6686.dat' 'tenx.input/matrix.mtx' && ln -s '/galaxy/server/database/objects/c/1/5/dataset_c15c1f7a-58b3-4992-b0aa-9dc0109eb36c.dat' 'tenx.input/genes.tsv' && ln -s '/galaxy/server/database/objects/5/6/f/dataset_56feca53-3171-4a60-9a60-b6a697dd5e66.dat' 'tenx.input/barcodes.tsv' && Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/a9caad671439/dropletutils/scripts/dropletutils.Rscript' '/galaxy/server/database/jobs_directory/000/147/configs/tmpvm7aa98f'", "user_email": "tests@fake.org", "command_version": "grep: invalid option -- 'P'\nBusyBox v1.22.1 (2014-05-23 01:24:27 UTC) multi-call binary.\n\nUsage: grep [-HhnlLoqvsriwFE] [-m N] [-A/B/C N] PATTERN/-e PATTERN.../-f FILE [FILE]...\n\nSearch for PATTERN in FILEs (or stdin)\n\n\t-H\tAdd 'filename:' prefix\n\t-h\tDo not add 'filename:' prefix\n\t-n\tAdd 'line_no:' prefix\n\t-l\tShow only names of files that match\n\t-L\tShow only names of files that don't match\n\t-c\tShow only count of matching lines\n\t-o\tShow only the matching part of line\n\t-q\tQuiet. Return 0 if PATTERN is found, 1 otherwise\n\t-v\tSelect non-matching lines\n\t-s\tSuppress open and read errors\n\t-r\tRecurse\n\t-i\tIgnore case\n\t-w\tMatch whole words only\n\t-x\tMatch whole lines only\n\t-F\tPATTERN is a literal (not regexp)\n\t-E\tPATTERN is an extended regexp\n\t-m N\tMatch up to N times per file\n\t-A N\tPrint N lines of trailing context\n\t-B N\tPrint N lines of leading context\n\t-C N\tSame as '-A N -B N'\n\t-e PTRN\tPattern to match\n\t-f FILE\tRead pattern from file", "params": {"__input_ext": "\"mtx\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"100\"", "operation": "{\"__current_case__\": 0, \"method\": {\"__current_case__\": 0, \"expected\": \"3000\", \"lowerprop\": \"0.1\", \"upperquant\": \"0.99\", \"use\": \"defaultdrops\"}, \"outformat\": \"tsv\", \"use\": \"filter\"}", "tenx_format": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 225, \"src\": \"hda\"}]}, \"input_barcodes\": {\"values\": [{\"id\": 227, \"src\": \"hda\"}]}, \"input_genes\": {\"values\": [{\"id\": 226, \"src\": \"hda\"}]}, \"use\": \"directory\"}"}, "inputs": {"tenx_format|input": {"id": "ccee83cbcfb78bc9", "src": "hda", "uuid": "7e61ecaf-fa41-4a24-aa5c-dc3d9c4c6686"}, "tenx_format|input_genes": {"id": "ff87f8ffbc7820f9", "src": "hda", "uuid": "c15c1f7a-58b3-4992-b0aa-9dc0109eb36c"}, "tenx_format|input_barcodes": {"id": "d85a18590724a5b8", "src": "hda", "uuid": "56feca53-3171-4a60-9a60-b6a697dd5e66"}}, "outputs": {"fileout_tsv": {"id": "97723ee83231c09c", "src": "hda", "uuid": "4b6f49b7-6977-4999-9b3d-df7427dca4bb"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 1025\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 1025\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "11 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "11.0000000"}, {"title": "Job End Time", "value": "2024-09-22 19:13:35", "plugin": "core", "name": "end_epoch", "raw_value": "1727032415.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:13:24", "plugin": "core", "name": "start_epoch", "raw_value": "1727032404.0000000"}, {"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": "dropletutils/1.10.0+galaxy2-1", "has_data": true, "data": {"tool_id": "dropletutils", "tool_version": "1.10.0+galaxy2", "test_index": 1, "time_seconds": 14.53026556968689, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "dropletutils/1.10.0+galaxy2-2", "has_data": true, "data": {"tool_id": "dropletutils", "tool_version": "1.10.0+galaxy2", "test_index": 2, "time_seconds": 57.89869499206543, "inputs": {"tenx_format|input": {"src": "hda", "id": "d3696918bdf326fa"}, "tenx_format|input_genes": {"src": "hda", "id": "aef90ae402321712"}, "tenx_format|input_barcodes": {"src": "hda", "id": "b1bbf1f841334af1"}, "tenx_format|use": "directory", "operation|lower": "120", "operation|use": "barcode_rank"}, "job": {"model_class": "Job", "id": "0b1249106278121c", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:14:19.956173", "update_time": "2024-09-22T19:14:45.897612", "galaxy_version": "24.1", "external_id": "gxy-xg28z", "handler": null, "job_runner_name": null, "command_line": "mkdir 'tenx.input' && ln -s '/galaxy/server/database/objects/2/b/5/dataset_2b5f3bc1-fb0c-4544-8f9c-7893efcd9aae.dat' 'tenx.input/matrix.mtx' && ln -s '/galaxy/server/database/objects/a/8/7/dataset_a87aee24-6fd5-4bc4-bd03-1f1f185352af.dat' 'tenx.input/genes.tsv' && ln -s '/galaxy/server/database/objects/4/6/7/dataset_467e3786-496f-48dc-8fa7-294eb77f8543.dat' 'tenx.input/barcodes.tsv' && Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/a9caad671439/dropletutils/scripts/dropletutils.Rscript' '/galaxy/server/database/jobs_directory/000/151/configs/tmplk_yngvf'", "user_email": "tests@fake.org", "command_version": "grep: invalid option -- 'P'\nBusyBox v1.22.1 (2014-05-23 01:24:27 UTC) multi-call binary.\n\nUsage: grep [-HhnlLoqvsriwFE] [-m N] [-A/B/C N] PATTERN/-e PATTERN.../-f FILE [FILE]...\n\nSearch for PATTERN in FILEs (or stdin)\n\n\t-H\tAdd 'filename:' prefix\n\t-h\tDo not add 'filename:' prefix\n\t-n\tAdd 'line_no:' prefix\n\t-l\tShow only names of files that match\n\t-L\tShow only names of files that don't match\n\t-c\tShow only count of matching lines\n\t-o\tShow only the matching part of line\n\t-q\tQuiet. Return 0 if PATTERN is found, 1 otherwise\n\t-v\tSelect non-matching lines\n\t-s\tSuppress open and read errors\n\t-r\tRecurse\n\t-i\tIgnore case\n\t-w\tMatch whole words only\n\t-x\tMatch whole lines only\n\t-F\tPATTERN is a literal (not regexp)\n\t-E\tPATTERN is an extended regexp\n\t-m N\tMatch up to N times per file\n\t-A N\tPrint N lines of trailing context\n\t-B N\tPrint N lines of leading context\n\t-C N\tSame as '-A N -B N'\n\t-e PTRN\tPattern to match\n\t-f FILE\tRead pattern from file", "params": {"__input_ext": "\"mtx\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"100\"", "operation": "{\"__current_case__\": 1, \"lower\": \"120\", \"use\": \"barcode_rank\"}", "tenx_format": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 229, \"src\": \"hda\"}]}, \"input_barcodes\": {\"values\": [{\"id\": 231, \"src\": \"hda\"}]}, \"input_genes\": {\"values\": [{\"id\": 230, \"src\": \"hda\"}]}, \"use\": \"directory\"}"}, "inputs": {"tenx_format|input": {"id": "d3696918bdf326fa", "src": "hda", "uuid": "2b5f3bc1-fb0c-4544-8f9c-7893efcd9aae"}, "tenx_format|input_genes": {"id": "aef90ae402321712", "src": "hda", "uuid": "a87aee24-6fd5-4bc4-bd03-1f1f185352af"}, "tenx_format|input_barcodes": {"id": "b1bbf1f841334af1", "src": "hda", "uuid": "467e3786-496f-48dc-8fa7-294eb77f8543"}}, "outputs": {"plot": {"id": "80d69efcc6fc5d25", "src": "hda", "uuid": "58d84a9a-699c-448f-82fd-f096dd5bd9b1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[1] \"knee = 324 , inflection = 151\"\n", "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nWarning message:\nIn xy.coords(x, y, xlabel, ylabel, log) :\n 7432 y values <= 0 omitted from logarithmic plot\n", "job_stdout": "", "job_stderr": "", "stdout": "[1] \"knee = 324 , inflection = 151\"\n", "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nWarning message:\nIn xy.coords(x, y, xlabel, ylabel, log) :\n 7432 y values <= 0 omitted from logarithmic plot\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "11 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "11.0000000"}, {"title": "Job End Time", "value": "2024-09-22 19:14:32", "plugin": "core", "name": "end_epoch", "raw_value": "1727032472.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:14:21", "plugin": "core", "name": "start_epoch", "raw_value": "1727032461.0000000"}, {"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": "dropletutils/1.10.0+galaxy2-2", "has_data": true, "data": {"tool_id": "dropletutils", "tool_version": "1.10.0+galaxy2", "test_index": 2, "time_seconds": 46.42261528968811, "inputs": {"tenx_format|input": {"src": "hda", "id": "fdcac0a8c7aded9e"}, "tenx_format|input_genes": {"src": "hda", "id": "d822304ea4730230"}, "tenx_format|input_barcodes": {"src": "hda", "id": "dcc8128c9a302db5"}, "tenx_format|use": "directory", "operation|lower": "120", "operation|use": "barcode_rank"}, "job": {"model_class": "Job", "id": "69d1074d84fd8c41", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", "state": "error", "exit_code": null, "create_time": "2024-09-22T19:19:02.872642", "update_time": "2024-09-22T19:19:18.491792", "galaxy_version": "24.1", "external_id": "gxy-7svqp", "handler": null, "job_runner_name": null, "command_line": "mkdir 'tenx.input' && ln -s '/galaxy/server/database/objects/f/7/7/dataset_f776d0cb-c106-411c-9e7b-ef6850d588af.dat' 'tenx.input/matrix.mtx' && ln -s '/galaxy/server/database/objects/0/6/f/dataset_06f1f7f5-6ca8-46a7-9ecc-c72ef2db5086.dat' 'tenx.input/genes.tsv' && ln -s '/galaxy/server/database/objects/6/d/4/dataset_6d439c11-4e86-4758-80c5-6d7d9629abd9.dat' 'tenx.input/barcodes.tsv' && Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/a9caad671439/dropletutils/scripts/dropletutils.Rscript' '/galaxy/server/database/jobs_directory/000/170/configs/tmpzm0jjs6k'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"mtx\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"100\"", "operation": "{\"__current_case__\": 1, \"lower\": \"120\", \"use\": \"barcode_rank\"}", "tenx_format": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 254, \"src\": \"hda\"}]}, \"input_barcodes\": {\"values\": [{\"id\": 256, \"src\": \"hda\"}]}, \"input_genes\": {\"values\": [{\"id\": 255, \"src\": \"hda\"}]}, \"use\": \"directory\"}"}, "inputs": {"tenx_format|input": {"id": "fdcac0a8c7aded9e", "src": "hda", "uuid": "f776d0cb-c106-411c-9e7b-ef6850d588af"}, "tenx_format|input_genes": {"id": "d822304ea4730230", "src": "hda", "uuid": "06f1f7f5-6ca8-46a7-9ecc-c72ef2db5086"}, "tenx_format|input_barcodes": {"id": "dcc8128c9a302db5", "src": "hda", "uuid": "6d439c11-4e86-4758-80c5-6d7d9629abd9"}}, "outputs": {"plot": {"id": "bbb27daa31c0eea0", "src": "hda", "uuid": "eb862c3f-fba6-47c9-8752-78637ce1ee50"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[1] \"knee = 324 , inflection = 151\"\n", "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nWarning message:\nIn xy.coords(x, y, xlabel, ylabel, log) :\n 7432 y values <= 0 omitted from logarithmic plot\n", "job_stdout": null, "job_stderr": null, "stdout": "[1] \"knee = 324 , inflection = 151\"\n", "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nWarning message:\nIn xy.coords(x, y, xlabel, ylabel, log) :\n 7432 y values <= 0 omitted from logarithmic plot\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, exit_code: None, stderr: Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nWarning message:\nIn xy.coords(x, y, xlabel, ylabel, log) :\n 7432 y values <= 0 omitted from logarithmic plot\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, exit_code: None, stderr: Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nWarning message:\nIn xy.coords(x, y, xlabel, ylabel, log) :\n 7432 y values <= 0 omitted from logarithmic plot\n."], "status": "failure"}}, {"id": "dropletutils/1.10.0+galaxy2-3", "has_data": true, "data": {"tool_id": "dropletutils", "tool_version": "1.10.0+galaxy2", "test_index": 3, "time_seconds": 58.727219104766846, "inputs": {"tenx_format|input": {"src": "hda", "id": "40e576919a69cb10"}, "tenx_format|input_genes": {"src": "hda", "id": "32660858b21b53d9"}, "tenx_format|input_barcodes": {"src": "hda", "id": "5986f82247c85c44"}, "tenx_format|use": "directory", "operation|method|lower": "150", "operation|method|fdr_thresh": "0.02", "operation|method|use": "emptydrops", "operation|outformat": "h5", "operation|use": "filter"}, "job": {"model_class": "Job", "id": "02f38e9397fe15a2", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:15:17.062555", "update_time": "2024-09-22T19:15:43.944528", "galaxy_version": "24.1", "external_id": "gxy-mfk6l", "handler": null, "job_runner_name": null, "command_line": "mkdir 'tenx.input' && ln -s '/galaxy/server/database/objects/7/5/e/dataset_75e1e999-9269-41eb-afd1-9522a2799de8.dat' 'tenx.input/matrix.mtx' && ln -s '/galaxy/server/database/objects/0/2/d/dataset_02db4041-8c9f-4a8c-87a0-c90820e70007.dat' 'tenx.input/genes.tsv' && ln -s '/galaxy/server/database/objects/3/0/3/dataset_303667af-d156-48b6-9106-9c846e273c54.dat' 'tenx.input/barcodes.tsv' && Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/a9caad671439/dropletutils/scripts/dropletutils.Rscript' '/galaxy/server/database/jobs_directory/000/155/configs/tmpttxh0w4y'", "user_email": "tests@fake.org", "command_version": "grep: invalid option -- 'P'\nBusyBox v1.22.1 (2014-05-23 01:24:27 UTC) multi-call binary.\n\nUsage: grep [-HhnlLoqvsriwFE] [-m N] [-A/B/C N] PATTERN/-e PATTERN.../-f FILE [FILE]...\n\nSearch for PATTERN in FILEs (or stdin)\n\n\t-H\tAdd 'filename:' prefix\n\t-h\tDo not add 'filename:' prefix\n\t-n\tAdd 'line_no:' prefix\n\t-l\tShow only names of files that match\n\t-L\tShow only names of files that don't match\n\t-c\tShow only count of matching lines\n\t-o\tShow only the matching part of line\n\t-q\tQuiet. Return 0 if PATTERN is found, 1 otherwise\n\t-v\tSelect non-matching lines\n\t-s\tSuppress open and read errors\n\t-r\tRecurse\n\t-i\tIgnore case\n\t-w\tMatch whole words only\n\t-x\tMatch whole lines only\n\t-F\tPATTERN is a literal (not regexp)\n\t-E\tPATTERN is an extended regexp\n\t-m N\tMatch up to N times per file\n\t-A N\tPrint N lines of trailing context\n\t-B N\tPrint N lines of leading context\n\t-C N\tSame as '-A N -B N'\n\t-e PTRN\tPattern to match\n\t-f FILE\tRead pattern from file", "params": {"__input_ext": "\"mtx\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"100\"", "operation": "{\"__current_case__\": 0, \"method\": {\"__current_case__\": 1, \"fdr_thresh\": \"0.02\", \"lower\": \"150\", \"use\": \"emptydrops\"}, \"outformat\": \"h5\", \"use\": \"filter\"}", "tenx_format": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 233, \"src\": \"hda\"}]}, \"input_barcodes\": {\"values\": [{\"id\": 235, \"src\": \"hda\"}]}, \"input_genes\": {\"values\": [{\"id\": 234, \"src\": \"hda\"}]}, \"use\": \"directory\"}"}, "inputs": {"tenx_format|input": {"id": "40e576919a69cb10", "src": "hda", "uuid": "75e1e999-9269-41eb-afd1-9522a2799de8"}, "tenx_format|input_genes": {"id": "32660858b21b53d9", "src": "hda", "uuid": "02db4041-8c9f-4a8c-87a0-c90820e70007"}, "tenx_format|input_barcodes": {"id": "5986f82247c85c44", "src": "hda", "uuid": "303667af-d156-48b6-9106-9c846e273c54"}}, "outputs": {"fileout_h5": {"id": "ecbeec3d7bfa3f20", "src": "hda", "uuid": "43a7c944-ad0a-4692-b05c-0ea7d5396085"}, "plot": {"id": "17fb3e65cc5c90bf", "src": "hda", "uuid": "4ca441c2-bfe3-4042-ac42-a45f58ffad80"}, "table": {"id": "23fe8d2e8bed377e", "src": "hda", "uuid": "2af30fec-6e6f-46b0-826d-ec6243c15ed3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[1] \"Cell Library Size Distribution:\"\n Min. 1st Qu. Median Mean 3rd Qu. Max. \n 0.00 0.00 0.00 46.53 3.00 1153.00 \n", "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 998\nCells and Limited: 998\n", "job_stdout": "", "job_stderr": "", "stdout": "[1] \"Cell Library Size Distribution:\"\n Min. 1st Qu. Median Mean 3rd Qu. Max. \n 0.00 0.00 0.00 46.53 3.00 1153.00 \n", "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 998\nCells and Limited: 998\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": "2024-09-22 19:15:30", "plugin": "core", "name": "end_epoch", "raw_value": "1727032530.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:15:18", "plugin": "core", "name": "start_epoch", "raw_value": "1727032518.0000000"}, {"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": "dropletutils/1.10.0+galaxy2-3", "has_data": true, "data": {"tool_id": "dropletutils", "tool_version": "1.10.0+galaxy2", "test_index": 3, "time_seconds": 13.56270956993103, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "dropletutils/1.10.0+galaxy2-4", "has_data": true, "data": {"tool_id": "dropletutils", "tool_version": "1.10.0+galaxy2", "test_index": 4, "time_seconds": 44.996108531951904, "inputs": {"tenx_format|input": {"src": "hda", "id": "2e82e628690af495"}, "tenx_format|use": "h5", "operation|method|lower": "150", "operation|method|fdr_thresh": "0.02", "operation|method|use": "emptydrops", "operation|outformat": "h5", "operation|use": "filter"}, "job": {"model_class": "Job", "id": "00bf5e33f5f60a84", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", "state": "error", "exit_code": null, "create_time": "2024-09-22T19:16:09.360909", "update_time": "2024-09-22T19:16:29.622402", "galaxy_version": "24.1", "external_id": "gxy-r4m44", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/a9caad671439/dropletutils/scripts/dropletutils.Rscript' '/galaxy/server/database/jobs_directory/000/157/configs/tmpfdt0g2xt'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"h5\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"100\"", "operation": "{\"__current_case__\": 0, \"method\": {\"__current_case__\": 1, \"fdr_thresh\": \"0.02\", \"lower\": \"150\", \"use\": \"emptydrops\"}, \"outformat\": \"h5\", \"use\": \"filter\"}", "tenx_format": "{\"__current_case__\": 1, \"input\": {\"values\": [{\"id\": 239, \"src\": \"hda\"}]}, \"use\": \"h5\"}"}, "inputs": {"tenx_format|input": {"id": "2e82e628690af495", "src": "hda", "uuid": "55edb90b-5bb7-4496-a18a-d9fa3f535a94"}}, "outputs": {"fileout_h5": {"id": "24cc1dc6eaa8876f", "src": "hda", "uuid": "22598fa7-3f7c-4764-842e-089622eb9d10"}, "plot": {"id": "807bfe01e9a68c8e", "src": "hda", "uuid": "7906c188-bd71-4f7a-9151-2df05203f29e"}, "table": {"id": "a9e73c1f2c590fd8", "src": "hda", "uuid": "c5d79519-4992-4643-bfff-73421ab8e541"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[1] \"Cell Library Size Distribution:\"\n Min. 1st Qu. Median Mean 3rd Qu. Max. \n 0.0 8.0 20.0 114.3 46.0 2347.0 \n", "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 954\nCells and Limited: 85\n", "job_stdout": null, "job_stderr": null, "stdout": "[1] \"Cell Library Size Distribution:\"\n Min. 1st Qu. Median Mean 3rd Qu. Max. \n 0.0 8.0 20.0 114.3 46.0 2347.0 \n", "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 954\nCells and Limited: 85\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, exit_code: None, stderr: Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 954\nCells and Limited: 85\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, exit_code: None, stderr: Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 954\nCells and Limited: 85\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, exit_code: None, stderr: Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 954\nCells and Limited: 85\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2, exit_code: None, stderr: Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 954\nCells and Limited: 85\n."], "status": "failure"}}, {"id": "dropletutils/1.10.0+galaxy2-4", "has_data": true, "data": {"tool_id": "dropletutils", "tool_version": "1.10.0+galaxy2", "test_index": 4, "time_seconds": 54.60371732711792, "inputs": {"tenx_format|input": {"src": "hda", "id": "03c7147a7b2013d9"}, "tenx_format|use": "h5", "operation|method|lower": "150", "operation|method|fdr_thresh": "0.02", "operation|method|use": "emptydrops", "operation|outformat": "h5", "operation|use": "filter"}, "job": {"model_class": "Job", "id": "2f925a76a0742f8a", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:19:55.564588", "update_time": "2024-09-22T19:20:25.989737", "galaxy_version": "24.1", "external_id": "gxy-2v8zp", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/a9caad671439/dropletutils/scripts/dropletutils.Rscript' '/galaxy/server/database/jobs_directory/000/175/configs/tmpe22yhrdf'", "user_email": "tests@fake.org", "command_version": "grep: invalid option -- 'P'\nBusyBox v1.22.1 (2014-05-23 01:24:27 UTC) multi-call binary.\n\nUsage: grep [-HhnlLoqvsriwFE] [-m N] [-A/B/C N] PATTERN/-e PATTERN.../-f FILE [FILE]...\n\nSearch for PATTERN in FILEs (or stdin)\n\n\t-H\tAdd 'filename:' prefix\n\t-h\tDo not add 'filename:' prefix\n\t-n\tAdd 'line_no:' prefix\n\t-l\tShow only names of files that match\n\t-L\tShow only names of files that don't match\n\t-c\tShow only count of matching lines\n\t-o\tShow only the matching part of line\n\t-q\tQuiet. Return 0 if PATTERN is found, 1 otherwise\n\t-v\tSelect non-matching lines\n\t-s\tSuppress open and read errors\n\t-r\tRecurse\n\t-i\tIgnore case\n\t-w\tMatch whole words only\n\t-x\tMatch whole lines only\n\t-F\tPATTERN is a literal (not regexp)\n\t-E\tPATTERN is an extended regexp\n\t-m N\tMatch up to N times per file\n\t-A N\tPrint N lines of trailing context\n\t-B N\tPrint N lines of leading context\n\t-C N\tSame as '-A N -B N'\n\t-e PTRN\tPattern to match\n\t-f FILE\tRead pattern from file", "params": {"__input_ext": "\"h5\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"100\"", "operation": "{\"__current_case__\": 0, \"method\": {\"__current_case__\": 1, \"fdr_thresh\": \"0.02\", \"lower\": \"150\", \"use\": \"emptydrops\"}, \"outformat\": \"h5\", \"use\": \"filter\"}", "tenx_format": "{\"__current_case__\": 1, \"input\": {\"values\": [{\"id\": 261, \"src\": \"hda\"}]}, \"use\": \"h5\"}"}, "inputs": {"tenx_format|input": {"id": "03c7147a7b2013d9", "src": "hda", "uuid": "7e142f65-9ff2-4b83-b3a2-e5487b520d01"}}, "outputs": {"fileout_h5": {"id": "dc0e403caa69b4f1", "src": "hda", "uuid": "e29b668c-14c4-4601-9be6-9fc0af5d9559"}, "plot": {"id": "3a5b39c7e294d567", "src": "hda", "uuid": "aabd2b99-a07e-4d33-980d-f6bab0b4dec6"}, "table": {"id": "c9b3385b88b19a53", "src": "hda", "uuid": "07001fe4-1d94-45e9-918c-a9071c6cc460"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[1] \"Cell Library Size Distribution:\"\n Min. 1st Qu. Median Mean 3rd Qu. Max. \n 0.0 8.0 20.0 114.3 46.0 2347.0 \n", "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 954\nCells and Limited: 85\n", "job_stdout": "", "job_stderr": "", "stdout": "[1] \"Cell Library Size Distribution:\"\n Min. 1st Qu. Median Mean 3rd Qu. Max. \n 0.0 8.0 20.0 114.3 46.0 2347.0 \n", "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 954\nCells and Limited: 85\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "16 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "16.0000000"}, {"title": "Job End Time", "value": "2024-09-22 19:20:12", "plugin": "core", "name": "end_epoch", "raw_value": "1727032812.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:19:56", "plugin": "core", "name": "start_epoch", "raw_value": "1727032796.0000000"}, {"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": "dropletutils/1.10.0+galaxy2-5", "has_data": true, "data": {"tool_id": "dropletutils", "tool_version": "1.10.0+galaxy2", "test_index": 5, "time_seconds": 51.36277937889099, "inputs": {"tenx_format|input": {"src": "hda", "id": "abb9b62407fe0ce9"}, "tenx_format|use": "tsv", "operation|method|expected": "2000", "operation|method|upperquant": "0.85", "operation|method|use": "defaultdrops", "operation|outformat": "directory", "operation|use": "filter"}, "job": {"model_class": "Job", "id": "400fd7205f084227", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:16:54.313410", "update_time": "2024-09-22T19:17:20.296017", "galaxy_version": "24.1", "external_id": "gxy-z4td7", "handler": null, "job_runner_name": null, "command_line": "mkdir 'tenx.output' && Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/a9caad671439/dropletutils/scripts/dropletutils.Rscript' '/galaxy/server/database/jobs_directory/000/159/configs/tmpve5wg50g'", "user_email": "tests@fake.org", "command_version": "grep: invalid option -- 'P'\nBusyBox v1.22.1 (2014-05-23 01:24:27 UTC) multi-call binary.\n\nUsage: grep [-HhnlLoqvsriwFE] [-m N] [-A/B/C N] PATTERN/-e PATTERN.../-f FILE [FILE]...\n\nSearch for PATTERN in FILEs (or stdin)\n\n\t-H\tAdd 'filename:' prefix\n\t-h\tDo not add 'filename:' prefix\n\t-n\tAdd 'line_no:' prefix\n\t-l\tShow only names of files that match\n\t-L\tShow only names of files that don't match\n\t-c\tShow only count of matching lines\n\t-o\tShow only the matching part of line\n\t-q\tQuiet. Return 0 if PATTERN is found, 1 otherwise\n\t-v\tSelect non-matching lines\n\t-s\tSuppress open and read errors\n\t-r\tRecurse\n\t-i\tIgnore case\n\t-w\tMatch whole words only\n\t-x\tMatch whole lines only\n\t-F\tPATTERN is a literal (not regexp)\n\t-E\tPATTERN is an extended regexp\n\t-m N\tMatch up to N times per file\n\t-A N\tPrint N lines of trailing context\n\t-B N\tPrint N lines of leading context\n\t-C N\tSame as '-A N -B N'\n\t-e PTRN\tPattern to match\n\t-f FILE\tRead pattern from file", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"100\"", "operation": "{\"__current_case__\": 0, \"method\": {\"__current_case__\": 0, \"expected\": \"2000\", \"lowerprop\": \"0.1\", \"upperquant\": \"0.85\", \"use\": \"defaultdrops\"}, \"outformat\": \"directory\", \"use\": \"filter\"}", "tenx_format": "{\"__current_case__\": 2, \"input\": {\"values\": [{\"id\": 243, \"src\": \"hda\"}]}, \"use\": \"tsv\"}"}, "inputs": {"tenx_format|input": {"id": "abb9b62407fe0ce9", "src": "hda", "uuid": "a14577cf-ec2f-405f-b7df-d6aeafe9bb9a"}}, "outputs": {"barcodes_out": {"id": "ec0e0eb53459707b", "src": "hda", "uuid": "7e9dde59-9c0f-4411-ad1c-eb9e0237098c"}, "genes_out": {"id": "07428d147d3f998b", "src": "hda", "uuid": "871a078d-b3a4-4b66-8e8f-62e39f86681f"}, "matrix_out": {"id": "776b24154498ea97", "src": "hda", "uuid": "8fa398da-d8ef-46ad-841c-c3273c2096ca"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 2650\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 2650\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "11 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "11.0000000"}, {"title": "Job End Time", "value": "2024-09-22 19:17:07", "plugin": "core", "name": "end_epoch", "raw_value": "1727032627.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:16:56", "plugin": "core", "name": "start_epoch", "raw_value": "1727032616.0000000"}, {"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": "dropletutils/1.10.0+galaxy2-5", "has_data": true, "data": {"tool_id": "dropletutils", "tool_version": "1.10.0+galaxy2", "test_index": 5, "time_seconds": 51.934855937957764, "inputs": {"tenx_format|input": {"src": "hda", "id": "f9a25e820a151a47"}, "tenx_format|use": "tsv", "operation|method|expected": "2000", "operation|method|upperquant": "0.85", "operation|method|use": "defaultdrops", "operation|outformat": "directory", "operation|use": "filter"}, "job": {"model_class": "Job", "id": "1ac46435ea78d248", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:20:51.527517", "update_time": "2024-09-22T19:21:17.640981", "galaxy_version": "24.1", "external_id": "gxy-fjn87", "handler": null, "job_runner_name": null, "command_line": "mkdir 'tenx.output' && Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/a9caad671439/dropletutils/scripts/dropletutils.Rscript' '/galaxy/server/database/jobs_directory/000/177/configs/tmp9zdbh2dq'", "user_email": "tests@fake.org", "command_version": "grep: invalid option -- 'P'\nBusyBox v1.22.1 (2014-05-23 01:24:27 UTC) multi-call binary.\n\nUsage: grep [-HhnlLoqvsriwFE] [-m N] [-A/B/C N] PATTERN/-e PATTERN.../-f FILE [FILE]...\n\nSearch for PATTERN in FILEs (or stdin)\n\n\t-H\tAdd 'filename:' prefix\n\t-h\tDo not add 'filename:' prefix\n\t-n\tAdd 'line_no:' prefix\n\t-l\tShow only names of files that match\n\t-L\tShow only names of files that don't match\n\t-c\tShow only count of matching lines\n\t-o\tShow only the matching part of line\n\t-q\tQuiet. Return 0 if PATTERN is found, 1 otherwise\n\t-v\tSelect non-matching lines\n\t-s\tSuppress open and read errors\n\t-r\tRecurse\n\t-i\tIgnore case\n\t-w\tMatch whole words only\n\t-x\tMatch whole lines only\n\t-F\tPATTERN is a literal (not regexp)\n\t-E\tPATTERN is an extended regexp\n\t-m N\tMatch up to N times per file\n\t-A N\tPrint N lines of trailing context\n\t-B N\tPrint N lines of leading context\n\t-C N\tSame as '-A N -B N'\n\t-e PTRN\tPattern to match\n\t-f FILE\tRead pattern from file", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"100\"", "operation": "{\"__current_case__\": 0, \"method\": {\"__current_case__\": 0, \"expected\": \"2000\", \"lowerprop\": \"0.1\", \"upperquant\": \"0.85\", \"use\": \"defaultdrops\"}, \"outformat\": \"directory\", \"use\": \"filter\"}", "tenx_format": "{\"__current_case__\": 2, \"input\": {\"values\": [{\"id\": 265, \"src\": \"hda\"}]}, \"use\": \"tsv\"}"}, "inputs": {"tenx_format|input": {"id": "f9a25e820a151a47", "src": "hda", "uuid": "25d54173-c778-41b3-8327-0d686b78fdae"}}, "outputs": {"barcodes_out": {"id": "6a7a21fd2860a981", "src": "hda", "uuid": "8c88e95e-3562-4e36-9237-641444e2138a"}, "genes_out": {"id": "423c230e955d7976", "src": "hda", "uuid": "46db65aa-84f1-4a0c-a864-d0a63b6ed6f9"}, "matrix_out": {"id": "041fd024214f1b9d", "src": "hda", "uuid": "814457ed-e777-47d6-ad70-309be42319f3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 2650\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Error in print.default(ifelse(is.na(y), NA_character_, sQuote(y)), quote = FALSE, : \n ignoring SIGPIPE signal\nCalls: -> print.numeric_version -> print -> print.default\nExecution halted\nCells: 2650\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "10 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "10.0000000"}, {"title": "Job End Time", "value": "2024-09-22 19:21:03", "plugin": "core", "name": "end_epoch", "raw_value": "1727032863.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:20:53", "plugin": "core", "name": "start_epoch", "raw_value": "1727032853.0000000"}, {"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": "fastp/0.23.4+galaxy1-0", "has_data": true, "data": {"tool_id": "fastp", "tool_version": "0.23.4+galaxy1", "test_index": 0, "time_seconds": 31.612127542495728, "inputs": {"single_paired|in1": {"src": "hda", "id": "969e5d311cab4b80"}, "single_paired|single_paired_selector": "single"}, "job": {"model_class": "Job", "id": "969e5d311cab4b80", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-09-22T18:36:00.876879", "update_time": "2024-09-22T18:36:09.259177", "galaxy_version": "24.1", "external_id": "gxy-dlhzs", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/9/3/7/dataset_93748e78-babf-44f0-803d-d018408ff776.dat' 'R1_fq.fastq' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for R1_fq.fastq' -i 'R1_fq.fastq' -o first.fastq && mv first.fastq '/galaxy/server/database/objects/4/0/8/dataset_408e1ff7-1252-43ea-8228-26f1b7aeef45.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"single_paired": "{\"__current_case__\": 0, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_tail1\": \"\"}, \"in1\": {\"values\": [{\"id\": 10, \"src\": \"hda\"}]}, \"single_paired_selector\": \"single\"}", "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 1, \"poly_g_min_len\": \"\", \"trimming_select\": \"\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": false, \"umi_len\": \"\", \"umi_loc\": null, \"umi_prefix\": null}}", "output_options": "{\"report_html\": true, \"report_json\": false}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"single_paired|in1": {"id": "969e5d311cab4b80", "src": "hda", "uuid": "93748e78-babf-44f0-803d-d018408ff776"}}, "outputs": {"report_html": {"id": "91c44c78512c30a5", "src": "hda", "uuid": "a3a55db8-8f57-46eb-8f17-72002b84caef"}, "out1": {"id": "674e1020fd2ef73d", "src": "hda", "uuid": "408e1ff7-1252-43ea-8228-26f1b7aeef45"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq \nfastp v0.23.4, time used: 1 seconds\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq \nfastp v0.23.4, time used: 1 seconds\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, exit_code: None, stderr: Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq \nfastp v0.23.4, time used: 1 seconds\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, exit_code: None, stderr: Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq \nfastp v0.23.4, time used: 1 seconds\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, exit_code: None, stderr: Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq \nfastp v0.23.4, time used: 1 seconds\n."], "status": "failure"}}, {"id": "fastp/0.23.4+galaxy1-1", "has_data": true, "data": {"tool_id": "fastp", "tool_version": "0.23.4+galaxy1", "test_index": 1, "time_seconds": 30.68775987625122, "inputs": {"single_paired|paired_input": {"src": "hdca", "id": "b2116f9eb07476cf"}, "single_paired|single_paired_selector": "paired_collection"}, "job": {"model_class": "Job", "id": "d759c259412d2085", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-09-22T18:36:33.485539", "update_time": "2024-09-22T18:36:39.552742", "galaxy_version": "24.1", "external_id": "gxy-d2qls", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/e/6/1/dataset_e61dd1bd-fc1c-471c-bc70-3f5fb7feead8.dat' 'Unnamed Collection.fastq' && ln -sf '/galaxy/server/database/objects/6/7/c/dataset_67cc8ba1-b5bd-4b51-958f-e6178e55d257.dat' 'Unnamed Collection_R2.fastq' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for Unnamed Collection.fastq' -i 'Unnamed Collection.fastq' -o first.fastq -I 'Unnamed Collection_R2.fastq' -O second.fastq && mv first.fastq '/galaxy/server/database/objects/4/c/8/dataset_4c8e8c27-c50b-45f7-aa7e-828119ce7302.dat' && mv second.fastq '/galaxy/server/database/objects/c/d/8/dataset_cd86ba74-decc-4625-8923-ddc02b44fc8d.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"single_paired": "{\"__current_case__\": 2, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"adapter_sequence2\": null, \"detect_adapter_for_pe\": false, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_front2\": \"\", \"trim_tail1\": \"\", \"trim_tail2\": \"\"}, \"paired_input\": {\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}, \"single_paired_selector\": \"paired_collection\"}", "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 1, \"poly_g_min_len\": \"\", \"trimming_select\": \"\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": false, \"umi_len\": \"\", \"umi_loc\": null, \"umi_prefix\": null}}", "output_options": "{\"report_html\": true, \"report_json\": false}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"single_paired|paired_input2": {"id": "681ebc328158e387", "src": "hda", "uuid": "67cc8ba1-b5bd-4b51-958f-e6178e55d257"}, "single_paired|paired_input1": {"id": "d759c259412d2085", "src": "hda", "uuid": "e61dd1bd-fc1c-471c-bc70-3f5fb7feead8"}}, "outputs": {"report_html": {"id": "7adda38f44fa79e6", "src": "hda", "uuid": "281df2db-101f-4c40-b836-64c1d2db2cfb"}, "output_paired_coll|__part__|reverse": {"id": "4db39dbef52fde2f", "src": "hda", "uuid": "cd86ba74-decc-4625-8923-ddc02b44fc8d"}, "output_paired_coll|__part__|forward": {"id": "10acb56af84768f5", "src": "hda", "uuid": "4c8e8c27-c50b-45f7-aa7e-828119ce7302"}}, "copied_from_job_id": null, "output_collections": {"output_paired_coll": {"src": "hdca", "id": "ab630ae25a673765"}}, "tool_stdout": "", "tool_stderr": "Read1 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 23268(93.6376%)\nQ30 bases: 22391(90.1083%)\n\nRead2 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 22676(91.2552%)\nQ30 bases: 21532(86.6514%)\n\nRead1 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21680(94.4992%)\nQ30 bases: 20981(91.4524%)\n\nRead2 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21535(93.8671%)\nQ30 bases: 20672(90.1055%)\n\nFiltering result:\nreads passed filter: 194\nreads failed due to low quality: 2\nreads failed due to too many N: 2\nreads failed due to too short: 0\nreads with adapter trimmed: 68\nbases trimmed due to adapters: 2824\n\nDuplication rate: 0%\n\nInsert size peak (evaluated by paired-end reads): 308\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for Unnamed Collection.fastq -i Unnamed Collection.fastq -o first.fastq -I Unnamed Collection_R2.fastq -O second.fastq \nfastp v0.23.4, time used: 1 seconds\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "Read1 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 23268(93.6376%)\nQ30 bases: 22391(90.1083%)\n\nRead2 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 22676(91.2552%)\nQ30 bases: 21532(86.6514%)\n\nRead1 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21680(94.4992%)\nQ30 bases: 20981(91.4524%)\n\nRead2 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21535(93.8671%)\nQ30 bases: 20672(90.1055%)\n\nFiltering result:\nreads passed filter: 194\nreads failed due to low quality: 2\nreads failed due to too many N: 2\nreads failed due to too short: 0\nreads with adapter trimmed: 68\nbases trimmed due to adapters: 2824\n\nDuplication rate: 0%\n\nInsert size peak (evaluated by paired-end reads): 308\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for Unnamed Collection.fastq -i Unnamed Collection.fastq -o first.fastq -I Unnamed Collection_R2.fastq -O second.fastq \nfastp v0.23.4, time used: 1 seconds\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, exit_code: None, stderr: Read1 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 23268(93.6376%)\nQ30 bases: 22391(90.1083%)\n\nRead2 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 22676(91.2552%)\nQ30 bases: 21532(86.6514%)\n\nRead1 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21680(94.4992%)\nQ30 bases: 20981(91.4524%)\n\nRead2 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21535(93.8671%)\nQ30 bases: 20672(90.1055%)\n\nFiltering result:\nreads passed filter: 194\nreads failed due to low quality: 2\nreads failed due to too many N: 2\nreads failed due to too short: 0\nreads with adapter trimmed: 68\nbases trimmed due to adapters: 2824\n\nDuplication rate: 0%\n\nInsert size peak (evaluated by paired-end reads): 308\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for Unnamed Collection.fastq -i Unnamed Collection.fastq -o first.fastq -I Unnamed Collection_R2.fastq -O second.fastq \nfastp v0.23.4, time used: 1 seconds\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1, exit_code: None, stderr: Read1 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 23268(93.6376%)\nQ30 bases: 22391(90.1083%)\n\nRead2 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 22676(91.2552%)\nQ30 bases: 21532(86.6514%)\n\nRead1 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21680(94.4992%)\nQ30 bases: 20981(91.4524%)\n\nRead2 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21535(93.8671%)\nQ30 bases: 20672(90.1055%)\n\nFiltering result:\nreads passed filter: 194\nreads failed due to low quality: 2\nreads failed due to too many N: 2\nreads failed due to too short: 0\nreads with adapter trimmed: 68\nbases trimmed due to adapters: 2824\n\nDuplication rate: 0%\n\nInsert size peak (evaluated by paired-end reads): 308\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for Unnamed Collection.fastq -i Unnamed Collection.fastq -o first.fastq -I Unnamed Collection_R2.fastq -O second.fastq \nfastp v0.23.4, time used: 1 seconds\n."], "status": "failure"}}, {"id": "fastp/0.23.4+galaxy1-10", "has_data": true, "data": {"tool_id": "fastp", "tool_version": "0.23.4+galaxy1", "test_index": 10, "time_seconds": 39.32555866241455, "inputs": {"single_paired|in1": {"src": "hda", "id": "c6c8fb4a58b3f660"}, "single_paired|single_paired_selector": "single", "read_mod_options|polyg_tail_trimming|trimming_select": "-G", "read_mod_options|polyx_tail_trimming|poly_x_min_len": "10", "read_mod_options|polyx_tail_trimming|polyx_trimming_select": "-x"}, "job": {"model_class": "Job", "id": "7c5815f4e6458210", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:42:27.162157", "update_time": "2024-09-22T18:42:43.120539", "galaxy_version": "24.1", "external_id": "gxy-fxlxq", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/4/c/6/dataset_4c63db3f-1e7e-444b-bd43-03532456ac44.dat' 'R1_fq_gz.fastq.gz' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for R1_fq_gz.fastq.gz' -i 'R1_fq_gz.fastq.gz' -o first.fastq.gz -x --poly_x_min_len 10 && mv first.fastq.gz '/galaxy/server/database/objects/f/3/8/dataset_f3859ef3-1377-400b-bbec-6a5e06b146a6.dat'", "user_email": "tests@fake.org", "command_version": "fastp 0.23.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_options": "{\"report_html\": true, \"report_json\": false}", "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 2, \"trimming_select\": \"-G\"}, \"polyx_tail_trimming\": {\"__current_case__\": 0, \"poly_x_min_len\": \"10\", \"polyx_trimming_select\": \"-x\"}, \"umi_processing\": {\"umi\": false, \"umi_len\": \"\", \"umi_loc\": null, \"umi_prefix\": null}}", "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", "single_paired": "{\"__current_case__\": 0, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_tail1\": \"\"}, \"in1\": {\"values\": [{\"id\": 48, \"src\": \"hda\"}]}, \"single_paired_selector\": \"single\"}"}, "inputs": {"single_paired|in1": {"id": "c6c8fb4a58b3f660", "src": "hda", "uuid": "4c63db3f-1e7e-444b-bd43-03532456ac44"}}, "outputs": {"out1": {"id": "6cc1d9b362dc16df", "src": "hda", "uuid": "f3859ef3-1377-400b-bbec-6a5e06b146a6"}, "report_html": {"id": "1356c91b4121b106", "src": "hda", "uuid": "bdd080ba-23af-493e-856f-efb2c2ffacaa"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\nreads with polyX in 3' end: 0\nbases trimmed in polyX tail: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq_gz.fastq.gz -i R1_fq_gz.fastq.gz -o first.fastq.gz -x --poly_x_min_len 10 \nfastp v0.23.4, time used: 1 seconds\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\nreads with polyX in 3' end: 0\nbases trimmed in polyX tail: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq_gz.fastq.gz -i R1_fq_gz.fastq.gz -o first.fastq.gz -x --poly_x_min_len 10 \nfastp v0.23.4, time used: 1 seconds\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:42:28", "plugin": "core", "name": "start_epoch", "raw_value": "1727030548.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:42:30", "plugin": "core", "name": "end_epoch", "raw_value": "1727030550.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "fastp/0.23.4+galaxy1-11", "has_data": true, "data": {"tool_id": "fastp", "tool_version": "0.23.4+galaxy1", "test_index": 11, "time_seconds": 39.33359122276306, "inputs": {"single_paired|paired_input": {"src": "hdca", "id": "e4e0e9adb4a70f5d"}, "single_paired|single_paired_selector": "paired_collection"}, "job": {"model_class": "Job", "id": "f460fb6ee726512e", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "state": "error", "exit_code": 255, "create_time": "2024-09-22T18:43:07.768195", "update_time": "2024-09-22T18:43:22.893312", "galaxy_version": "24.1", "external_id": "gxy-767g9", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/c/6/d/dataset_c6df2c59-d07b-4247-b6cf-0f52c8818ca9.dat' 'Unnamed Collection.fastq' && ln -sf '/galaxy/server/database/objects/7/2/0/dataset_72074a2f-62f9-45ff-b5e7-ab01d0cb2c3b.dat' 'Unnamed Collection_R2.fastq' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for Unnamed Collection.fastq' -i 'Unnamed Collection.fastq' -o first.fastq -I 'Unnamed Collection_R2.fastq' -O second.fastq && mv first.fastq '/galaxy/server/database/objects/8/d/8/dataset_8d80d5b6-a9d8-42f4-b9ea-5e1095e22e1c.dat' && mv second.fastq '/galaxy/server/database/objects/c/e/5/dataset_ce5560a4-4b37-4703-a8eb-e11d117ffe0b.dat'", "user_email": "tests@fake.org", "command_version": "fastp 0.23.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_options": "{\"report_html\": true, \"report_json\": false}", "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 1, \"poly_g_min_len\": \"\", \"trimming_select\": \"\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": false, \"umi_len\": \"\", \"umi_loc\": null, \"umi_prefix\": null}}", "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", "single_paired": "{\"__current_case__\": 2, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"adapter_sequence2\": null, \"detect_adapter_for_pe\": false, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_front2\": \"\", \"trim_tail1\": \"\", \"trim_tail2\": \"\"}, \"paired_input\": {\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}, \"single_paired_selector\": \"paired_collection\"}"}, "inputs": {"single_paired|paired_input1": {"id": "0c0369322ab0183a", "src": "hda", "uuid": "c6df2c59-d07b-4247-b6cf-0f52c8818ca9"}, "single_paired|paired_input2": {"id": "df041e0a5e2a496e", "src": "hda", "uuid": "72074a2f-62f9-45ff-b5e7-ab01d0cb2c3b"}}, "outputs": {"output_paired_coll|__part__|forward": {"id": "ce67f983aab93dca", "src": "hda", "uuid": "8d80d5b6-a9d8-42f4-b9ea-5e1095e22e1c"}, "output_paired_coll|__part__|reverse": {"id": "6d6283e6a8a1dd61", "src": "hda", "uuid": "ce5560a4-4b37-4703-a8eb-e11d117ffe0b"}, "report_html": {"id": "57b30d8abe5104ed", "src": "hda", "uuid": "657721a4-9a11-4b8b-820c-74c731ee44a2"}}, "copied_from_job_id": null, "output_collections": {"output_paired_coll": {"src": "hdca", "id": "22bd9d5c76a71522"}}, "tool_stdout": "", "tool_stderr": "\nWARNNIG: different read numbers of the 0 pack\nRead1 pack size: 99\nRead2 pack size: 100\n\nERROR: input files don't contain identical amount of reads\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "\nWARNNIG: different read numbers of the 0 pack\nRead1 pack size: 99\nRead2 pack size: 100\n\nERROR: input files don't contain identical amount of reads\n", "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 255 ()", "error_level": 3, "exit_code": 255, "type": "exit_code"}], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:43:09", "plugin": "core", "name": "start_epoch", "raw_value": "1727030589.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:43:10", "plugin": "core", "name": "end_epoch", "raw_value": "1727030590.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastp/0.23.4+galaxy1-2", "has_data": true, "data": {"tool_id": "fastp", "tool_version": "0.23.4+galaxy1", "test_index": 2, "time_seconds": 38.67101049423218, "inputs": {"single_paired|in1": {"src": "hda", "id": "253bda685e8b739e"}, "single_paired|adapter_trimming_options|adapter_sequence1": "ATCG", "single_paired|single_paired_selector": "single"}, "job": {"model_class": "Job", "id": "10acb56af84768f5", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:37:02.656008", "update_time": "2024-09-22T18:37:18.464038", "galaxy_version": "24.1", "external_id": "gxy-6lzjk", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/a/2/8/dataset_a28a5068-caa2-4b87-ad34-a36b77be9ed7.dat' 'R1_fq.fastq' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for R1_fq.fastq' -i 'R1_fq.fastq' -o first.fastq --adapter_sequence 'ATCG' && mv first.fastq '/galaxy/server/database/objects/1/3/e/dataset_13e951e7-f800-4de0-a97c-2991d43f6dc2.dat'", "user_email": "tests@fake.org", "command_version": "fastp 0.23.4", "params": {"single_paired": "{\"__current_case__\": 0, \"adapter_trimming_options\": {\"adapter_sequence1\": \"ATCG\", \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_tail1\": \"\"}, \"in1\": {\"values\": [{\"id\": 18, \"src\": \"hda\"}]}, \"single_paired_selector\": \"single\"}", "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 1, \"poly_g_min_len\": \"\", \"trimming_select\": \"\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": false, \"umi_len\": \"\", \"umi_loc\": null, \"umi_prefix\": null}}", "output_options": "{\"report_html\": true, \"report_json\": false}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"single_paired|in1": {"id": "253bda685e8b739e", "src": "hda", "uuid": "a28a5068-caa2-4b87-ad34-a36b77be9ed7"}}, "outputs": {"out1": {"id": "828bfa29cbdba689", "src": "hda", "uuid": "13e951e7-f800-4de0-a97c-2991d43f6dc2"}, "report_html": {"id": "5a16ec0aa88259c3", "src": "hda", "uuid": "ba04530f-aa69-4a2a-8560-bf9e754a9ce0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Read1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 1\ntotal bases: 151\nQ20 bases: 114(75.4967%)\nQ30 bases: 98(64.9007%)\n\nFiltering result:\nreads passed filter: 1\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 1\nreads with adapter trimmed: 1\nbases trimmed due to adapters: 139\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq --adapter_sequence ATCG \nfastp v0.23.4, time used: 1 seconds\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Read1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 1\ntotal bases: 151\nQ20 bases: 114(75.4967%)\nQ30 bases: 98(64.9007%)\n\nFiltering result:\nreads passed filter: 1\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 1\nreads with adapter trimmed: 1\nbases trimmed due to adapters: 139\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq --adapter_sequence ATCG \nfastp v0.23.4, time used: 1 seconds\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:37:04", "plugin": "core", "name": "start_epoch", "raw_value": "1727030224.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:37:05", "plugin": "core", "name": "end_epoch", "raw_value": "1727030225.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastp/0.23.4+galaxy1-3", "has_data": true, "data": {"tool_id": "fastp", "tool_version": "0.23.4+galaxy1", "test_index": 3, "time_seconds": 40.604599475860596, "inputs": {"single_paired|in1": {"src": "hda", "id": "7b0eb28556b65bbc"}, "single_paired|single_paired_selector": "single", "read_mod_options|umi_processing|umi": true, "read_mod_options|umi_processing|umi_loc": "read1", "read_mod_options|umi_processing|umi_len": "8"}, "job": {"model_class": "Job", "id": "7adda38f44fa79e6", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:37:42.969860", "update_time": "2024-09-22T18:37:59.114965", "galaxy_version": "24.1", "external_id": "gxy-qssrf", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/0/7/5/dataset_075f506e-2d15-43d3-883c-cf4cf367cf4b.dat' 'R1_fq.fastq' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for R1_fq.fastq' -i 'R1_fq.fastq' -o first.fastq -U --umi_loc 'read1' --umi_len 8 && mv first.fastq '/galaxy/server/database/objects/f/9/e/dataset_f9e617de-e844-42df-b6d1-ffb3a633d9a0.dat'", "user_email": "tests@fake.org", "command_version": "fastp 0.23.4", "params": {"overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", "single_paired": "{\"__current_case__\": 0, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_tail1\": \"\"}, \"in1\": {\"values\": [{\"id\": 21, \"src\": \"hda\"}]}, \"single_paired_selector\": \"single\"}", "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 1, \"poly_g_min_len\": \"\", \"trimming_select\": \"\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": true, \"umi_len\": \"8\", \"umi_loc\": \"read1\", \"umi_prefix\": null}}", "output_options": "{\"report_html\": true, \"report_json\": false}", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"single_paired|in1": {"id": "7b0eb28556b65bbc", "src": "hda", "uuid": "075f506e-2d15-43d3-883c-cf4cf367cf4b"}}, "outputs": {"out1": {"id": "96fbcb20aca29e32", "src": "hda", "uuid": "f9e617de-e844-42df-b6d1-ffb3a633d9a0"}, "report_html": {"id": "35fa0402327a6eb3", "src": "hda", "uuid": "6a06fcfc-8fd4-455c-9462-375dd0c01117"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 286\nQ20 bases: 246(86.014%)\nQ30 bases: 226(79.021%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq -U --umi_loc read1 --umi_len 8 \nfastp v0.23.4, time used: 1 seconds\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 286\nQ20 bases: 246(86.014%)\nQ30 bases: 226(79.021%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq -U --umi_loc read1 --umi_len 8 \nfastp v0.23.4, time used: 1 seconds\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:37:44", "plugin": "core", "name": "start_epoch", "raw_value": "1727030264.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:37:45", "plugin": "core", "name": "end_epoch", "raw_value": "1727030265.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastp/0.23.4+galaxy1-4", "has_data": true, "data": {"tool_id": "fastp", "tool_version": "0.23.4+galaxy1", "test_index": 4, "time_seconds": 43.73406267166138, "inputs": {"single_paired|in1": {"src": "hda", "id": "466b21d6567c1a8b"}, "single_paired|single_paired_selector": "single", "read_mod_options|umi_processing|umi": true, "read_mod_options|umi_processing|umi_loc": "read1", "read_mod_options|umi_processing|umi_len": "12"}, "job": {"model_class": "Job", "id": "828bfa29cbdba689", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:38:26.769682", "update_time": "2024-09-22T18:38:42.855029", "galaxy_version": "24.1", "external_id": "gxy-tv8hc", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/1/b/1/dataset_1b1ad02c-8e8e-476e-af5c-ef3f5fd65eb9.dat' 'R1_fq.fastq' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for R1_fq.fastq' -i 'R1_fq.fastq' -o first.fastq -U --umi_loc 'read1' --umi_len 12 && mv first.fastq '/galaxy/server/database/objects/7/b/3/dataset_7b33dcfd-8f1b-429d-97f2-ac7fc7ff96f5.dat'", "user_email": "tests@fake.org", "command_version": "fastp 0.23.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_options": "{\"report_html\": true, \"report_json\": false}", "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 1, \"poly_g_min_len\": \"\", \"trimming_select\": \"\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": true, \"umi_len\": \"12\", \"umi_loc\": \"read1\", \"umi_prefix\": null}}", "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", "single_paired": "{\"__current_case__\": 0, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_tail1\": \"\"}, \"in1\": {\"values\": [{\"id\": 24, \"src\": \"hda\"}]}, \"single_paired_selector\": \"single\"}"}, "inputs": {"single_paired|in1": {"id": "466b21d6567c1a8b", "src": "hda", "uuid": "1b1ad02c-8e8e-476e-af5c-ef3f5fd65eb9"}}, "outputs": {"out1": {"id": "013447f2159c7372", "src": "hda", "uuid": "7b33dcfd-8f1b-429d-97f2-ac7fc7ff96f5"}, "report_html": {"id": "c4dc9a3ed0350f1d", "src": "hda", "uuid": "98b81f75-eabb-4913-8e99-fa880dc0ee54"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 278\nQ20 bases: 239(85.9712%)\nQ30 bases: 220(79.1367%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq -U --umi_loc read1 --umi_len 12 \nfastp v0.23.4, time used: 1 seconds\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 278\nQ20 bases: 239(85.9712%)\nQ30 bases: 220(79.1367%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq -U --umi_loc read1 --umi_len 12 \nfastp v0.23.4, time used: 1 seconds\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:38:28", "plugin": "core", "name": "start_epoch", "raw_value": "1727030308.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:38:29", "plugin": "core", "name": "end_epoch", "raw_value": "1727030309.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastp/0.23.4+galaxy1-5", "has_data": true, "data": {"tool_id": "fastp", "tool_version": "0.23.4+galaxy1", "test_index": 5, "time_seconds": 40.86374807357788, "inputs": {"single_paired|in1": {"src": "hda", "id": "aa8a6ac0e00d78ad"}, "single_paired|in2": {"src": "hda", "id": "de3c3af45053bfd8"}, "single_paired|single_paired_selector": "paired"}, "job": {"model_class": "Job", "id": "96fbcb20aca29e32", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:39:06.313480", "update_time": "2024-09-22T18:39:23.652651", "galaxy_version": "24.1", "external_id": "gxy-sk8sx", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/b/d/c/dataset_bdc56c12-c875-4289-abfc-e40a04245d25.dat' 'bwa-mem-fastq1_fq.fastq' && ln -sf '/galaxy/server/database/objects/6/d/9/dataset_6d9639bd-d26b-403f-8cec-66db3b4d5ab6.dat' 'bwa-mem-fastq2_fq_R2.fastq' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for bwa-mem-fastq1_fq.fastq' -i 'bwa-mem-fastq1_fq.fastq' -o first.fastq -I 'bwa-mem-fastq2_fq_R2.fastq' -O second.fastq && mv first.fastq '/galaxy/server/database/objects/c/6/f/dataset_c6fa2363-493a-449a-8b0e-eae8967f952b.dat' && mv second.fastq '/galaxy/server/database/objects/2/2/3/dataset_223cec16-88d0-4444-84cc-4878be8c7a7e.dat'", "user_email": "tests@fake.org", "command_version": "fastp 0.23.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_options": "{\"report_html\": true, \"report_json\": false}", "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 1, \"poly_g_min_len\": \"\", \"trimming_select\": \"\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": false, \"umi_len\": \"\", \"umi_loc\": null, \"umi_prefix\": null}}", "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", "single_paired": "{\"__current_case__\": 1, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"adapter_sequence2\": null, \"detect_adapter_for_pe\": false, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_front2\": \"\", \"trim_tail1\": \"\", \"trim_tail2\": \"\"}, \"in1\": {\"values\": [{\"id\": 27, \"src\": \"hda\"}]}, \"in2\": {\"values\": [{\"id\": 28, \"src\": \"hda\"}]}, \"single_paired_selector\": \"paired\"}"}, "inputs": {"single_paired|in1": {"id": "aa8a6ac0e00d78ad", "src": "hda", "uuid": "bdc56c12-c875-4289-abfc-e40a04245d25"}, "single_paired|in2": {"id": "de3c3af45053bfd8", "src": "hda", "uuid": "6d9639bd-d26b-403f-8cec-66db3b4d5ab6"}}, "outputs": {"out1": {"id": "4861b7d962feb9bc", "src": "hda", "uuid": "c6fa2363-493a-449a-8b0e-eae8967f952b"}, "out2": {"id": "32fa6d0d322d9ba7", "src": "hda", "uuid": "223cec16-88d0-4444-84cc-4878be8c7a7e"}, "report_html": {"id": "0e7b444bf5eb7e3c", "src": "hda", "uuid": "0340d87a-4ea1-47a0-a7ac-11730057df8a"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Read1 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 23268(93.6376%)\nQ30 bases: 22391(90.1083%)\n\nRead2 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 22676(91.2552%)\nQ30 bases: 21532(86.6514%)\n\nRead1 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21680(94.4992%)\nQ30 bases: 20981(91.4524%)\n\nRead2 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21535(93.8671%)\nQ30 bases: 20672(90.1055%)\n\nFiltering result:\nreads passed filter: 194\nreads failed due to low quality: 2\nreads failed due to too many N: 2\nreads failed due to too short: 0\nreads with adapter trimmed: 68\nbases trimmed due to adapters: 2824\n\nDuplication rate: 0%\n\nInsert size peak (evaluated by paired-end reads): 308\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for bwa-mem-fastq1_fq.fastq -i bwa-mem-fastq1_fq.fastq -o first.fastq -I bwa-mem-fastq2_fq_R2.fastq -O second.fastq \nfastp v0.23.4, time used: 1 seconds\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Read1 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 23268(93.6376%)\nQ30 bases: 22391(90.1083%)\n\nRead2 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 22676(91.2552%)\nQ30 bases: 21532(86.6514%)\n\nRead1 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21680(94.4992%)\nQ30 bases: 20981(91.4524%)\n\nRead2 after filtering:\ntotal reads: 97\ntotal bases: 22942\nQ20 bases: 21535(93.8671%)\nQ30 bases: 20672(90.1055%)\n\nFiltering result:\nreads passed filter: 194\nreads failed due to low quality: 2\nreads failed due to too many N: 2\nreads failed due to too short: 0\nreads with adapter trimmed: 68\nbases trimmed due to adapters: 2824\n\nDuplication rate: 0%\n\nInsert size peak (evaluated by paired-end reads): 308\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for bwa-mem-fastq1_fq.fastq -i bwa-mem-fastq1_fq.fastq -o first.fastq -I bwa-mem-fastq2_fq_R2.fastq -O second.fastq \nfastp v0.23.4, time used: 1 seconds\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:39:08", "plugin": "core", "name": "start_epoch", "raw_value": "1727030348.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:39:09", "plugin": "core", "name": "end_epoch", "raw_value": "1727030349.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastp/0.23.4+galaxy1-6", "has_data": true, "data": {"tool_id": "fastp", "tool_version": "0.23.4+galaxy1", "test_index": 6, "time_seconds": 41.56670022010803, "inputs": {"single_paired|in1": {"src": "hda", "id": "3ba0663152f4bf6e"}, "single_paired|in2": {"src": "hda", "id": "a004fae819566744"}, "single_paired|single_paired_selector": "paired", "read_mod_options|umi_processing|umi": true, "read_mod_options|umi_processing|umi_loc": "read1", "read_mod_options|umi_processing|umi_len": "8"}, "job": {"model_class": "Job", "id": "013447f2159c7372", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:39:48.138548", "update_time": "2024-09-22T18:40:04.944527", "galaxy_version": "24.1", "external_id": "gxy-bq5ff", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/3/0/4/dataset_304c591c-4266-48c3-be3b-95d070d6caea.dat' 'bwa-mem-fastq1_fq.fastq' && ln -sf '/galaxy/server/database/objects/e/4/7/dataset_e4715584-c1f3-489f-a41e-d20ed4d759fb.dat' 'bwa-mem-fastq2_fq_R2.fastq' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for bwa-mem-fastq1_fq.fastq' -i 'bwa-mem-fastq1_fq.fastq' -o first.fastq -I 'bwa-mem-fastq2_fq_R2.fastq' -O second.fastq -U --umi_loc 'read1' --umi_len 8 && mv first.fastq '/galaxy/server/database/objects/3/2/f/dataset_32fd942c-7ebb-4ee0-adb7-76e11832beb6.dat' && mv second.fastq '/galaxy/server/database/objects/f/d/0/dataset_fd050891-257d-46d4-aef6-5b2cdf6b644b.dat'", "user_email": "tests@fake.org", "command_version": "fastp 0.23.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_options": "{\"report_html\": true, \"report_json\": false}", "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 1, \"poly_g_min_len\": \"\", \"trimming_select\": \"\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": true, \"umi_len\": \"8\", \"umi_loc\": \"read1\", \"umi_prefix\": null}}", "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", "single_paired": "{\"__current_case__\": 1, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"adapter_sequence2\": null, \"detect_adapter_for_pe\": false, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_front2\": \"\", \"trim_tail1\": \"\", \"trim_tail2\": \"\"}, \"in1\": {\"values\": [{\"id\": 32, \"src\": \"hda\"}]}, \"in2\": {\"values\": [{\"id\": 33, \"src\": \"hda\"}]}, \"single_paired_selector\": \"paired\"}"}, "inputs": {"single_paired|in1": {"id": "3ba0663152f4bf6e", "src": "hda", "uuid": "304c591c-4266-48c3-be3b-95d070d6caea"}, "single_paired|in2": {"id": "a004fae819566744", "src": "hda", "uuid": "e4715584-c1f3-489f-a41e-d20ed4d759fb"}}, "outputs": {"out1": {"id": "7c5815f4e6458210", "src": "hda", "uuid": "32fd942c-7ebb-4ee0-adb7-76e11832beb6"}, "out2": {"id": "b96af63d7deb5821", "src": "hda", "uuid": "fd050891-257d-46d4-aef6-5b2cdf6b644b"}, "report_html": {"id": "7d986344f3cd03cd", "src": "hda", "uuid": "a7f656f3-b8f2-4515-9edf-73f75d3eaf27"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Read1 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 23268(93.6376%)\nQ30 bases: 22391(90.1083%)\n\nRead2 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 22676(91.2552%)\nQ30 bases: 21532(86.6514%)\n\nRead1 after filtering:\ntotal reads: 97\ntotal bases: 22166\nQ20 bases: 20935(94.4464%)\nQ30 bases: 20255(91.3787%)\n\nRead2 after filtering:\ntotal reads: 97\ntotal bases: 22646\nQ20 bases: 21284(93.9857%)\nQ30 bases: 20447(90.2897%)\n\nFiltering result:\nreads passed filter: 194\nreads failed due to low quality: 2\nreads failed due to too many N: 2\nreads failed due to too short: 0\nreads with adapter trimmed: 76\nbases trimmed due to adapters: 3128\n\nDuplication rate: 0%\n\nInsert size peak (evaluated by paired-end reads): 243\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for bwa-mem-fastq1_fq.fastq -i bwa-mem-fastq1_fq.fastq -o first.fastq -I bwa-mem-fastq2_fq_R2.fastq -O second.fastq -U --umi_loc read1 --umi_len 8 \nfastp v0.23.4, time used: 1 seconds\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Read1 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 23268(93.6376%)\nQ30 bases: 22391(90.1083%)\n\nRead2 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 22676(91.2552%)\nQ30 bases: 21532(86.6514%)\n\nRead1 after filtering:\ntotal reads: 97\ntotal bases: 22166\nQ20 bases: 20935(94.4464%)\nQ30 bases: 20255(91.3787%)\n\nRead2 after filtering:\ntotal reads: 97\ntotal bases: 22646\nQ20 bases: 21284(93.9857%)\nQ30 bases: 20447(90.2897%)\n\nFiltering result:\nreads passed filter: 194\nreads failed due to low quality: 2\nreads failed due to too many N: 2\nreads failed due to too short: 0\nreads with adapter trimmed: 76\nbases trimmed due to adapters: 3128\n\nDuplication rate: 0%\n\nInsert size peak (evaluated by paired-end reads): 243\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for bwa-mem-fastq1_fq.fastq -i bwa-mem-fastq1_fq.fastq -o first.fastq -I bwa-mem-fastq2_fq_R2.fastq -O second.fastq -U --umi_loc read1 --umi_len 8 \nfastp v0.23.4, time used: 1 seconds\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:39:49", "plugin": "core", "name": "start_epoch", "raw_value": "1727030389.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:39:50", "plugin": "core", "name": "end_epoch", "raw_value": "1727030390.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastp/0.23.4+galaxy1-7", "has_data": true, "data": {"tool_id": "fastp", "tool_version": "0.23.4+galaxy1", "test_index": 7, "time_seconds": 40.57904028892517, "inputs": {"single_paired|in1": {"src": "hda", "id": "f460fb6ee726512e"}, "single_paired|in2": {"src": "hda", "id": "3079a032fd721413"}, "single_paired|single_paired_selector": "paired", "read_mod_options|umi_processing|umi": true, "read_mod_options|umi_processing|umi_loc": "read2", "read_mod_options|umi_processing|umi_len": "8"}, "job": {"model_class": "Job", "id": "de3c3af45053bfd8", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:40:30.498170", "update_time": "2024-09-22T18:40:45.932743", "galaxy_version": "24.1", "external_id": "gxy-5fnfb", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/0/f/c/dataset_0fc3a0ea-b747-49ff-ba80-990275ea195e.dat' 'bwa-mem-fastq1_fq.fastq' && ln -sf '/galaxy/server/database/objects/0/1/a/dataset_01a0a9d8-9bc6-4ba7-a024-9f25f20444b8.dat' 'bwa-mem-fastq2_fq_R2.fastq' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for bwa-mem-fastq1_fq.fastq' -i 'bwa-mem-fastq1_fq.fastq' -o first.fastq -I 'bwa-mem-fastq2_fq_R2.fastq' -O second.fastq -U --umi_loc 'read2' --umi_len 8 && mv first.fastq '/galaxy/server/database/objects/5/a/3/dataset_5a378320-4ffc-46cb-844b-3dfa1c4ec56c.dat' && mv second.fastq '/galaxy/server/database/objects/0/c/3/dataset_0c390a4e-3099-4195-9b32-3c2b4288509d.dat'", "user_email": "tests@fake.org", "command_version": "fastp 0.23.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_options": "{\"report_html\": true, \"report_json\": false}", "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 1, \"poly_g_min_len\": \"\", \"trimming_select\": \"\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": true, \"umi_len\": \"8\", \"umi_loc\": \"read2\", \"umi_prefix\": null}}", "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", "single_paired": "{\"__current_case__\": 1, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"adapter_sequence2\": null, \"detect_adapter_for_pe\": false, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_front2\": \"\", \"trim_tail1\": \"\", \"trim_tail2\": \"\"}, \"in1\": {\"values\": [{\"id\": 37, \"src\": \"hda\"}]}, \"in2\": {\"values\": [{\"id\": 38, \"src\": \"hda\"}]}, \"single_paired_selector\": \"paired\"}"}, "inputs": {"single_paired|in2": {"id": "3079a032fd721413", "src": "hda", "uuid": "01a0a9d8-9bc6-4ba7-a024-9f25f20444b8"}, "single_paired|in1": {"id": "f460fb6ee726512e", "src": "hda", "uuid": "0fc3a0ea-b747-49ff-ba80-990275ea195e"}}, "outputs": {"out1": {"id": "8341ef21327c738f", "src": "hda", "uuid": "5a378320-4ffc-46cb-844b-3dfa1c4ec56c"}, "out2": {"id": "2cfcc8703d27f0e5", "src": "hda", "uuid": "0c390a4e-3099-4195-9b32-3c2b4288509d"}, "report_html": {"id": "dfbed326cfd5efc6", "src": "hda", "uuid": "a77708d8-a799-49ae-8062-ad941b5d758d"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Read1 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 23268(93.6376%)\nQ30 bases: 22391(90.1083%)\n\nRead2 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 22676(91.2552%)\nQ30 bases: 21532(86.6514%)\n\nRead1 after filtering:\ntotal reads: 97\ntotal bases: 22678\nQ20 bases: 21439(94.5366%)\nQ30 bases: 20756(91.5248%)\n\nRead2 after filtering:\ntotal reads: 97\ntotal bases: 22166\nQ20 bases: 20766(93.684%)\nQ30 bases: 19910(89.8223%)\n\nFiltering result:\nreads passed filter: 194\nreads failed due to low quality: 2\nreads failed due to too many N: 2\nreads failed due to too short: 0\nreads with adapter trimmed: 68\nbases trimmed due to adapters: 3096\n\nDuplication rate: 0%\n\nInsert size peak (evaluated by paired-end reads): 300\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for bwa-mem-fastq1_fq.fastq -i bwa-mem-fastq1_fq.fastq -o first.fastq -I bwa-mem-fastq2_fq_R2.fastq -O second.fastq -U --umi_loc read2 --umi_len 8 \nfastp v0.23.4, time used: 1 seconds\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Read1 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 23268(93.6376%)\nQ30 bases: 22391(90.1083%)\n\nRead2 before filtering:\ntotal reads: 99\ntotal bases: 24849\nQ20 bases: 22676(91.2552%)\nQ30 bases: 21532(86.6514%)\n\nRead1 after filtering:\ntotal reads: 97\ntotal bases: 22678\nQ20 bases: 21439(94.5366%)\nQ30 bases: 20756(91.5248%)\n\nRead2 after filtering:\ntotal reads: 97\ntotal bases: 22166\nQ20 bases: 20766(93.684%)\nQ30 bases: 19910(89.8223%)\n\nFiltering result:\nreads passed filter: 194\nreads failed due to low quality: 2\nreads failed due to too many N: 2\nreads failed due to too short: 0\nreads with adapter trimmed: 68\nbases trimmed due to adapters: 3096\n\nDuplication rate: 0%\n\nInsert size peak (evaluated by paired-end reads): 300\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for bwa-mem-fastq1_fq.fastq -i bwa-mem-fastq1_fq.fastq -o first.fastq -I bwa-mem-fastq2_fq_R2.fastq -O second.fastq -U --umi_loc read2 --umi_len 8 \nfastp v0.23.4, time used: 1 seconds\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:40:32", "plugin": "core", "name": "start_epoch", "raw_value": "1727030432.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:40:33", "plugin": "core", "name": "end_epoch", "raw_value": "1727030433.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastp/0.23.4+galaxy1-8", "has_data": true, "data": {"tool_id": "fastp", "tool_version": "0.23.4+galaxy1", "test_index": 8, "time_seconds": 38.36762261390686, "inputs": {"single_paired|in1": {"src": "hda", "id": "f905a481a4b06e29"}, "single_paired|single_paired_selector": "single", "output_options|report_html": false, "output_options|report_json": true}, "job": {"model_class": "Job", "id": "32fa6d0d322d9ba7", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:41:09.323755", "update_time": "2024-09-22T18:41:24.412597", "galaxy_version": "24.1", "external_id": "gxy-9t7d6", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/4/4/5/dataset_445ba5e5-d8d6-4078-9057-00b684601ab8.dat' 'R1_fq.fastq' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for R1_fq.fastq' -i 'R1_fq.fastq' -o first.fastq && mv first.fastq '/galaxy/server/database/objects/b/b/1/dataset_bb1754d2-13f9-48b1-854d-1d8b93db59e4.dat'", "user_email": "tests@fake.org", "command_version": "fastp 0.23.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_options": "{\"report_html\": false, \"report_json\": true}", "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 1, \"poly_g_min_len\": \"\", \"trimming_select\": \"\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": false, \"umi_len\": \"\", \"umi_loc\": null, \"umi_prefix\": null}}", "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", "single_paired": "{\"__current_case__\": 0, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_tail1\": \"\"}, \"in1\": {\"values\": [{\"id\": 42, \"src\": \"hda\"}]}, \"single_paired_selector\": \"single\"}"}, "inputs": {"single_paired|in1": {"id": "f905a481a4b06e29", "src": "hda", "uuid": "445ba5e5-d8d6-4078-9057-00b684601ab8"}}, "outputs": {"out1": {"id": "56205cc7e82f9ae3", "src": "hda", "uuid": "bb1754d2-13f9-48b1-854d-1d8b93db59e4"}, "report_json": {"id": "0dc46b40c8f13446", "src": "hda", "uuid": "77b8cf98-690b-43a7-89ec-1a7de2c60bec"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq \nfastp v0.23.4, time used: 1 seconds\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq \nfastp v0.23.4, time used: 1 seconds\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:41:10", "plugin": "core", "name": "start_epoch", "raw_value": "1727030470.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:41:11", "plugin": "core", "name": "end_epoch", "raw_value": "1727030471.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "fastp/0.23.4+galaxy1-9", "has_data": true, "data": {"tool_id": "fastp", "tool_version": "0.23.4+galaxy1", "test_index": 9, "time_seconds": 39.03892517089844, "inputs": {"single_paired|in1": {"src": "hda", "id": "9def34d8cdf7f887"}, "single_paired|single_paired_selector": "single", "read_mod_options|polyg_tail_trimming|poly_g_min_len": "10", "read_mod_options|polyg_tail_trimming|trimming_select": "-g"}, "job": {"model_class": "Job", "id": "3ba0663152f4bf6e", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:41:47.738444", "update_time": "2024-09-22T18:42:03.804732", "galaxy_version": "24.1", "external_id": "gxy-g599k", "handler": null, "job_runner_name": null, "command_line": "ln -sf '/galaxy/server/database/objects/2/9/0/dataset_290c0d6e-9af6-48f9-ae4e-e2313e80d0ec.dat' 'R1_fq_gz.fastq.gz' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for R1_fq_gz.fastq.gz' -i 'R1_fq_gz.fastq.gz' -o first.fastq.gz --poly_g_min_len 10 -g && mv first.fastq.gz '/galaxy/server/database/objects/c/0/0/dataset_c003f290-413c-4ab0-a51d-5194c7a837e4.dat'", "user_email": "tests@fake.org", "command_version": "fastp 0.23.4", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_options": "{\"report_html\": true, \"report_json\": false}", "read_mod_options": "{\"base_correction_options\": {\"correction\": false}, \"cutting_by_quality_options\": {\"cut_by_quality3\": false, \"cut_by_quality5\": false, \"cut_mean_quality\": \"\", \"cut_window_size\": \"\"}, \"polyg_tail_trimming\": {\"__current_case__\": 0, \"poly_g_min_len\": \"10\", \"trimming_select\": \"-g\"}, \"polyx_tail_trimming\": {\"__current_case__\": 1, \"polyx_trimming_select\": \"\"}, \"umi_processing\": {\"umi\": false, \"umi_len\": \"\", \"umi_loc\": null, \"umi_prefix\": null}}", "filter_options": "{\"length_filtering_options\": {\"disable_length_filtering\": false, \"length_limit\": \"\", \"length_required\": \"\"}, \"low_complexity_filter\": {\"complexity_threshold\": \"\", \"enable_low_complexity_filter\": false}, \"quality_filtering_options\": {\"disable_quality_filtering\": false, \"n_base_limit\": \"\", \"qualified_quality_phred\": \"\", \"unqualified_percent_limit\": \"\"}}", "overrepresented_sequence_analysis": "{\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": \"\"}", "single_paired": "{\"__current_case__\": 0, \"adapter_trimming_options\": {\"adapter_sequence1\": null, \"disable_adapter_trimming\": false}, \"global_trimming_options\": {\"trim_front1\": \"\", \"trim_tail1\": \"\"}, \"in1\": {\"values\": [{\"id\": 45, \"src\": \"hda\"}]}, \"single_paired_selector\": \"single\"}"}, "inputs": {"single_paired|in1": {"id": "9def34d8cdf7f887", "src": "hda", "uuid": "290c0d6e-9af6-48f9-ae4e-e2313e80d0ec"}}, "outputs": {"out1": {"id": "5a762030bf60013d", "src": "hda", "uuid": "c003f290-413c-4ab0-a51d-5194c7a837e4"}, "report_html": {"id": "aed013ae912ac323", "src": "hda", "uuid": "663d9ba4-8d7f-4341-8a1f-d52871f6c151"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq_gz.fastq.gz -i R1_fq_gz.fastq.gz -o first.fastq.gz --poly_g_min_len 10 -g \nfastp v0.23.4, time used: 1 seconds\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Detecting adapter sequence for read1...\nNo adapter detected for read1\n\nRead1 before filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nRead1 after filtering:\ntotal reads: 2\ntotal bases: 302\nQ20 bases: 262(86.755%)\nQ30 bases: 241(79.8013%)\n\nFiltering result:\nreads passed filter: 2\nreads failed due to low quality: 0\nreads failed due to too many N: 0\nreads failed due to too short: 0\nreads with adapter trimmed: 0\nbases trimmed due to adapters: 0\n\nDuplication rate (may be overestimated since this is SE data): 0%\n\nJSON report: fastp.json\nHTML report: fastp.html\n\nfastp --thread 4 --report_title fastp report for R1_fq_gz.fastq.gz -i R1_fq_gz.fastq.gz -o first.fastq.gz --poly_g_min_len 10 -g \nfastp v0.23.4, time used: 1 seconds\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:41:49", "plugin": "core", "name": "start_epoch", "raw_value": "1727030509.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:41:50", "plugin": "core", "name": "end_epoch", "raw_value": "1727030510.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "pharmcat/1.7.0+galaxy0-0", "has_data": true, "data": {"tool_id": "pharmcat", "tool_version": "1.7.0+galaxy0", "test_index": 0, "time_seconds": 104.05597281455994, "inputs": {"function_select|input": {"src": "hda", "id": "f0f29fae8a930f62"}, "function_select|outside_call": {"src": "hda", "id": "4f4505a5a385d637"}, "function_select|json": true, "function_select|phenojson": true}, "job": {"model_class": "Job", "id": "0dc46b40c8f13446", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:45:34.535292", "update_time": "2024-09-22T18:46:54.097468", "galaxy_version": "24.1", "external_id": "gxy-89s8h", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/9/c/6/dataset_9c6b2b55-236b-4a66-a488-27b86d60bf4b.dat' ./input.vcf && java -jar /pharmcat/pharmcat.jar -vcf input.vcf -o output -f pharmCAT_report_Galaxy -a /galaxy/server/database/objects/2/2/d/dataset_22d4cd25-3408-4cb3-acd4-abab128b2ad3.dat -j -pj", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "function_select": "{\"__current_case__\": 0, \"function\": \"all\", \"input\": {\"values\": [{\"id\": 60, \"src\": \"hda\"}]}, \"json\": true, \"outside_call\": {\"values\": [{\"id\": 61, \"src\": \"hda\"}]}, \"phenojson\": true}"}, "inputs": {"function_select|outside_call": {"id": "4f4505a5a385d637", "src": "hda", "uuid": "22d4cd25-3408-4cb3-acd4-abab128b2ad3"}, "function_select|input": {"id": "f0f29fae8a930f62", "src": "hda", "uuid": "9c6b2b55-236b-4a66-a488-27b86d60bf4b"}}, "outputs": {"all_out": {"id": "24c429f3abbdf5b7", "src": "hda", "uuid": "21438863-33ce-4472-a453-c905dba82bfb"}, "all_pheno": {"id": "1fd8d0fa22e8bbdc", "src": "hda", "uuid": "8caa03b1-073e-4868-9af3-6222a8ec5b47"}, "all_out_json": {"id": "7de6a0f25fbb6c55", "src": "hda", "uuid": "de353c78-22bf-4af1-a439-59dbcfa56220"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Picked up _JAVA_OPTIONS: -Xmx4G -Xms1G\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Picked up _JAVA_OPTIONS: -Xmx4G -Xms1G\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:46:21", "plugin": "core", "name": "start_epoch", "raw_value": "1727030781.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:46:27", "plugin": "core", "name": "end_epoch", "raw_value": "1727030787.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}]}, "status": "success"}}, {"id": "pharmcat/1.7.0+galaxy0-1", "has_data": true, "data": {"tool_id": "pharmcat", "tool_version": "1.7.0+galaxy0", "test_index": 1, "time_seconds": 42.00770354270935, "inputs": {"function_select|input": {"src": "hda", "id": "66c8b670a8d53b88"}, "function_select|function": "name"}, "job": {"model_class": "Job", "id": "5a762030bf60013d", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:47:18.459913", "update_time": "2024-09-22T18:47:36.349264", "galaxy_version": "24.1", "external_id": "gxy-f7g47", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/7/1/f/dataset_71f859c4-6736-44a9-9474-7633e24dd1f8.dat' ./input.vcf && java -cp /pharmcat/pharmcat.jar org.pharmgkb.pharmcat.haplotype.NamedAlleleMatcher -vcf input.vcf -json output.json -html output.html", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "function_select": "{\"__current_case__\": 1, \"function\": \"name\", \"input\": {\"values\": [{\"id\": 65, \"src\": \"hda\"}]}}"}, "inputs": {"function_select|input": {"id": "66c8b670a8d53b88", "src": "hda", "uuid": "71f859c4-6736-44a9-9474-7633e24dd1f8"}}, "outputs": {"namer_html": {"id": "726baf7da75e24bf", "src": "hda", "uuid": "5b6b28c1-1b25-47a4-8708-65ef05dbe2f5"}, "namer_json": {"id": "7e8203a114c4f626", "src": "hda", "uuid": "36b01b9c-a405-45b6-b34e-6d84f91dfd87"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Picked up _JAVA_OPTIONS: -Xmx4G -Xms1G\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Picked up _JAVA_OPTIONS: -Xmx4G -Xms1G\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:47:20", "plugin": "core", "name": "start_epoch", "raw_value": "1727030840.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:47:22", "plugin": "core", "name": "end_epoch", "raw_value": "1727030842.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "pharmcat/1.7.0+galaxy0-2", "has_data": true, "data": {"tool_id": "pharmcat", "tool_version": "1.7.0+galaxy0", "test_index": 2, "time_seconds": 41.87273120880127, "inputs": {"function_select|method|input": {"src": "hda", "id": "ae77db7fb126134e"}, "function_select|method|pheno_function": "vcf", "function_select|outside_call": {"src": "hda", "id": "253ff2e3d2498d89"}, "function_select|function": "pheno"}, "job": {"model_class": "Job", "id": "6cc1d9b362dc16df", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:48:00.889149", "update_time": "2024-09-22T18:48:18.845819", "galaxy_version": "24.1", "external_id": "gxy-clkwd", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/0/5/1/dataset_0517bca4-b9de-4197-b5bc-7611778be2d7.dat' ./input.vcf && java -cp /pharmcat/pharmcat.jar org.pharmgkb.pharmcat.phenotype.Phenotyper -vcf input.vcf -o /galaxy/server/database/objects/9/b/a/dataset_9bafd6cc-eb46-4bb0-8c0e-9893889f2925.dat -f output.json", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "function_select": "{\"__current_case__\": 2, \"function\": \"pheno\", \"method\": {\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 68, \"src\": \"hda\"}]}, \"pheno_function\": \"vcf\"}, \"outside_call\": {\"values\": [{\"id\": 69, \"src\": \"hda\"}]}}"}, "inputs": {"function_select|method|input": {"id": "ae77db7fb126134e", "src": "hda", "uuid": "0517bca4-b9de-4197-b5bc-7611778be2d7"}, "function_select|outside_call": {"id": "253ff2e3d2498d89", "src": "hda", "uuid": "9bafd6cc-eb46-4bb0-8c0e-9893889f2925"}}, "outputs": {"pheno_json": {"id": "d9084cdf69786976", "src": "hda", "uuid": "d93db193-9070-45f1-83c3-052326d315e6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Picked up _JAVA_OPTIONS: -Xmx4G -Xms1G\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Picked up _JAVA_OPTIONS: -Xmx4G -Xms1G\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:48:02", "plugin": "core", "name": "start_epoch", "raw_value": "1727030882.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:48:06", "plugin": "core", "name": "end_epoch", "raw_value": "1727030886.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "pharmcat/1.7.0+galaxy0-3", "has_data": true, "data": {"tool_id": "pharmcat", "tool_version": "1.7.0+galaxy0", "test_index": 3, "time_seconds": 41.88088846206665, "inputs": {"function_select|method|input": {"src": "hda", "id": "8e4840b30d1dbe5c"}, "function_select|method|pheno_function": "named", "function_select|function": "pheno"}, "job": {"model_class": "Job", "id": "0c0369322ab0183a", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:48:42.457476", "update_time": "2024-09-22T18:49:00.656421", "galaxy_version": "24.1", "external_id": "gxy-9jjjp", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/f/e/8/dataset_fe859c0c-6190-4077-989b-3c3150f2443d.dat' ./input.json && java -cp /pharmcat/pharmcat.jar org.pharmgkb.pharmcat.phenotype.Phenotyper -c input.json -f output.json", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "function_select": "{\"__current_case__\": 2, \"function\": \"pheno\", \"method\": {\"__current_case__\": 1, \"input\": {\"values\": [{\"id\": 71, \"src\": \"hda\"}]}, \"pheno_function\": \"named\"}, \"outside_call\": null}"}, "inputs": {"function_select|method|input": {"id": "8e4840b30d1dbe5c", "src": "hda", "uuid": "fe859c0c-6190-4077-989b-3c3150f2443d"}}, "outputs": {"pheno_json": {"id": "52b9b477c2a547a7", "src": "hda", "uuid": "f54a7a44-43b9-4cc0-8422-9815115bf739"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Picked up _JAVA_OPTIONS: -Xmx4G -Xms1G\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Picked up _JAVA_OPTIONS: -Xmx4G -Xms1G\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:48:44", "plugin": "core", "name": "start_epoch", "raw_value": "1727030924.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:48:47", "plugin": "core", "name": "end_epoch", "raw_value": "1727030927.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}]}, "status": "success"}}, {"id": "pharmcat/1.7.0+galaxy0-4", "has_data": true, "data": {"tool_id": "pharmcat", "tool_version": "1.7.0+galaxy0", "test_index": 4, "time_seconds": 43.04553842544556, "inputs": {"function_select|input": {"src": "hda", "id": "e9c3ca647496144d"}, "function_select|function": "report"}, "job": {"model_class": "Job", "id": "ce67f983aab93dca", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.7.0+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:49:25.138884", "update_time": "2024-09-22T18:49:43.291987", "galaxy_version": "24.1", "external_id": "gxy-f4j9z", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/f/e/b/dataset_febb4466-a5b7-44cd-9118-9d7d140d2dc1.dat' ./input.json && java -cp /pharmcat/pharmcat.jar org.pharmgkb.pharmcat.reporter.Reporter -p input.json -j output.json -o output.html", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "function_select": "{\"__current_case__\": 3, \"function\": \"report\", \"input\": {\"values\": [{\"id\": 73, \"src\": \"hda\"}]}, \"title\": null}"}, "inputs": {"function_select|input": {"id": "e9c3ca647496144d", "src": "hda", "uuid": "febb4466-a5b7-44cd-9118-9d7d140d2dc1"}}, "outputs": {"report_html": {"id": "596b455e6e142e71", "src": "hda", "uuid": "bc64b923-2431-4932-a2a2-e089beb976e5"}, "report_json": {"id": "f6900f26ee5ea357", "src": "hda", "uuid": "83cfe6e1-64a4-43a8-a8ae-ee6cfe38e613"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Picked up _JAVA_OPTIONS: -Xmx4G -Xms1G\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Picked up _JAVA_OPTIONS: -Xmx4G -Xms1G\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "4294", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4294.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:49:26", "plugin": "core", "name": "start_epoch", "raw_value": "1727030966.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:49:29", "plugin": "core", "name": "end_epoch", "raw_value": "1727030969.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}]}, "status": "success"}}, {"id": "poretools_events/0.6.1a1.1-0", "has_data": true, "data": {"tool_id": "poretools_events", "tool_version": "0.6.1a1.1", "test_index": 0, "time_seconds": 63.73656964302063, "inputs": {"input": {"src": "hda", "id": "6449e1892e61ee60"}, "precalled": false}, "job": {"model_class": "Job", "id": "8341ef21327c738f", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1", "state": "error", "exit_code": 1, "create_time": "2024-09-22T18:43:49.771041", "update_time": "2024-09-22T18:44:29.937202", "galaxy_version": "24.1", "external_id": "gxy-dtphr", "handler": null, "job_runner_name": null, "command_line": "poretools events '/galaxy/server/database/objects/3/e/e/dataset_3ee49bdd-4c53-41a8-9007-125f5af29eab.dat' > '/galaxy/server/database/objects/1/a/2/dataset_1a2da447-2fc9-4695-b6f1-b495553b6540.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fast5.tar\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "precalled": "false"}, "inputs": {"input": {"id": "6449e1892e61ee60", "src": "hda", "uuid": "3ee49bdd-4c53-41a8-9007-125f5af29eab"}}, "outputs": {"output": {"id": "2911bf8aae422578", "src": "hda", "uuid": "1a2da447-2fc9-4695-b6f1-b495553b6540"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/poretools\", line 11, in \n load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 543, in main\n args.func(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 55, in run_subtool\n submodule.run(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/events.py\", line 17, in run\n for fast5 in Fast5File.Fast5FileSet(args.files):\n File \"/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py\", line 110, in next\n shutil.rmtree(PORETOOLS_TMPDIR)\n File \"/usr/local/lib/python2.7/shutil.py\", line 261, in rmtree\n rmtree(fullname, ignore_errors, onerror)\n File \"/usr/local/lib/python2.7/shutil.py\", line 270, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File \"/usr/local/lib/python2.7/shutil.py\", line 268, in rmtree\n os.rmdir(path)\nOSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data'\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/poretools\", line 11, in \n load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 543, in main\n args.func(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 55, in run_subtool\n submodule.run(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/events.py\", line 17, in run\n for fast5 in Fast5File.Fast5FileSet(args.files):\n File \"/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py\", line 110, in next\n shutil.rmtree(PORETOOLS_TMPDIR)\n File \"/usr/local/lib/python2.7/shutil.py\", line 261, in rmtree\n rmtree(fullname, ignore_errors, onerror)\n File \"/usr/local/lib/python2.7/shutil.py\", line 270, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File \"/usr/local/lib/python2.7/shutil.py\", line 268, in rmtree\n os.rmdir(path)\nOSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data'\n", "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}, {"code_desc": "", "desc": "Fatal error: ", "error_level": 3, "match": "Error:", "stream": "stderr", "type": "regex"}], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:44:09", "plugin": "core", "name": "start_epoch", "raw_value": "1727030649.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:44:10", "plugin": "core", "name": "end_epoch", "raw_value": "1727030650.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, exit_code: 1, stderr: Traceback (most recent call last):\n File \"/usr/local/bin/poretools\", line 11, in \n load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 543, in main\n args.func(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 55, in run_subtool\n submodule.run(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/events.py\", line 17, in run\n for fast5 in Fast5File.Fast5FileSet(args.files):\n File \"/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py\", line 110, in next\n shutil.rmtree(PORETOOLS_TMPDIR)\n File \"/usr/local/lib/python2.7/shutil.py\", line 261, in rmtree\n rmtree(fullname, ignore_errors, onerror)\n File \"/usr/local/lib/python2.7/shutil.py\", line 270, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File \"/usr/local/lib/python2.7/shutil.py\", line 268, in rmtree\n os.rmdir(path)\nOSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data'\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, exit_code: 1, stderr: Traceback (most recent call last):\n File \"/usr/local/bin/poretools\", line 11, in \n load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 543, in main\n args.func(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 55, in run_subtool\n submodule.run(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/events.py\", line 17, in run\n for fast5 in Fast5File.Fast5FileSet(args.files):\n File \"/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py\", line 110, in next\n shutil.rmtree(PORETOOLS_TMPDIR)\n File \"/usr/local/lib/python2.7/shutil.py\", line 261, in rmtree\n rmtree(fullname, ignore_errors, onerror)\n File \"/usr/local/lib/python2.7/shutil.py\", line 270, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File \"/usr/local/lib/python2.7/shutil.py\", line 268, in rmtree\n os.rmdir(path)\nOSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data'\n."], "status": "failure"}}, {"id": "poretools_events/0.6.1a1.1-1", "has_data": true, "data": {"tool_id": "poretools_events", "tool_version": "0.6.1a1.1", "test_index": 1, "time_seconds": 39.92147493362427, "inputs": {"input": {"src": "hda", "id": "5257353c1238d09b"}, "precalled": true}, "job": {"model_class": "Job", "id": "dfbed326cfd5efc6", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1", "state": "error", "exit_code": 1, "create_time": "2024-09-22T18:44:53.441327", "update_time": "2024-09-22T18:45:09.790026", "galaxy_version": "24.1", "external_id": "gxy-p6hg6", "handler": null, "job_runner_name": null, "command_line": "poretools events --pre-basecalled '/galaxy/server/database/objects/0/6/3/dataset_063614bc-f4dd-4f64-889e-524e4cc70140.dat' > '/galaxy/server/database/objects/f/9/8/dataset_f98ad021-8ef5-40bc-af9d-622b1d5b02ff.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"fast5.tar\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "precalled": "true"}, "inputs": {"input": {"id": "5257353c1238d09b", "src": "hda", "uuid": "063614bc-f4dd-4f64-889e-524e4cc70140"}}, "outputs": {"output": {"id": "b39a57cfa0641e66", "src": "hda", "uuid": "f98ad021-8ef5-40bc-af9d-622b1d5b02ff"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/poretools\", line 11, in \n load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 543, in main\n args.func(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 55, in run_subtool\n submodule.run(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/events.py\", line 13, in run\n for fast5 in Fast5File.Fast5FileSet(args.files):\n File \"/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py\", line 110, in next\n shutil.rmtree(PORETOOLS_TMPDIR)\n File \"/usr/local/lib/python2.7/shutil.py\", line 261, in rmtree\n rmtree(fullname, ignore_errors, onerror)\n File \"/usr/local/lib/python2.7/shutil.py\", line 270, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File \"/usr/local/lib/python2.7/shutil.py\", line 268, in rmtree\n os.rmdir(path)\nOSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data'\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Traceback (most recent call last):\n File \"/usr/local/bin/poretools\", line 11, in \n load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 543, in main\n args.func(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 55, in run_subtool\n submodule.run(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/events.py\", line 13, in run\n for fast5 in Fast5File.Fast5FileSet(args.files):\n File \"/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py\", line 110, in next\n shutil.rmtree(PORETOOLS_TMPDIR)\n File \"/usr/local/lib/python2.7/shutil.py\", line 261, in rmtree\n rmtree(fullname, ignore_errors, onerror)\n File \"/usr/local/lib/python2.7/shutil.py\", line 270, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File \"/usr/local/lib/python2.7/shutil.py\", line 268, in rmtree\n os.rmdir(path)\nOSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data'\n", "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}, {"code_desc": "", "desc": "Fatal error: ", "error_level": 3, "match": "Error:", "stream": "stderr", "type": "regex"}], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "12240", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "12240.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:44:55", "plugin": "core", "name": "start_epoch", "raw_value": "1727030695.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:44:56", "plugin": "core", "name": "end_epoch", "raw_value": "1727030696.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}]}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, exit_code: 1, stderr: Traceback (most recent call last):\n File \"/usr/local/bin/poretools\", line 11, in \n load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 543, in main\n args.func(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 55, in run_subtool\n submodule.run(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/events.py\", line 13, in run\n for fast5 in Fast5File.Fast5FileSet(args.files):\n File \"/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py\", line 110, in next\n shutil.rmtree(PORETOOLS_TMPDIR)\n File \"/usr/local/lib/python2.7/shutil.py\", line 261, in rmtree\n rmtree(fullname, ignore_errors, onerror)\n File \"/usr/local/lib/python2.7/shutil.py\", line 270, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File \"/usr/local/lib/python2.7/shutil.py\", line 268, in rmtree\n os.rmdir(path)\nOSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data'\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.1, exit_code: 1, stderr: Traceback (most recent call last):\n File \"/usr/local/bin/poretools\", line 11, in \n load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 543, in main\n args.func(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py\", line 55, in run_subtool\n submodule.run(parser, args)\n File \"/usr/local/lib/python2.7/site-packages/poretools/events.py\", line 13, in run\n for fast5 in Fast5File.Fast5FileSet(args.files):\n File \"/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py\", line 110, in next\n shutil.rmtree(PORETOOLS_TMPDIR)\n File \"/usr/local/lib/python2.7/shutil.py\", line 261, in rmtree\n rmtree(fullname, ignore_errors, onerror)\n File \"/usr/local/lib/python2.7/shutil.py\", line 270, in rmtree\n onerror(os.rmdir, path, sys.exc_info())\n File \"/usr/local/lib/python2.7/shutil.py\", line 268, in rmtree\n os.rmdir(path)\nOSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data'\n."], "status": "failure"}}, {"id": "qualimap_bamqc/2.3+galaxy0-0", "has_data": true, "data": {"tool_id": "qualimap_bamqc", "tool_version": "2.3+galaxy0", "test_index": 0, "time_seconds": 14.298835515975952, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "qualimap_bamqc/2.3+galaxy0-1", "has_data": true, "data": {"tool_id": "qualimap_bamqc", "tool_version": "2.3+galaxy0", "test_index": 1, "time_seconds": 83.5841383934021, "inputs": {"input1": {"src": "hda", "id": "29d0911801055dab"}, "per_base_coverage": true}, "job": {"model_class": "Job", "id": "6449e1892e61ee60", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:50:24.656320", "update_time": "2024-09-22T18:51:21.627694", "galaxy_version": "24.1", "external_id": "gxy-52nzh", "handler": null, "job_runner_name": null, "command_line": "export JAVA_OPTS=\"-Djava.awt.headless=true -Xmx${GALAXY_MEMORY_MB:-1024}m\" && ln -s '/galaxy/server/database/objects/d/f/1/dataset_df12f0ab-0792-4bc0-892b-90760cc67a2e.dat' 'test_mapped_reads_bam' && qualimap bamqc -bam 'test_mapped_reads_bam' -outdir results -outformat html --collect-overlap-pairs --output-genome-coverage results/coverage.txt -nw 400 --paint-chromosome-limits -hm 3 --skip-duplicated --skip-dup-mode 0 -nt ${GALAXY_SLOTS:-1} && mv results/coverage.txt '/galaxy/server/database/objects/e/7/8/dataset_e783cbbc-5e15-4a47-b41c-b52de419ccc5.dat' && sed 's|images_qualimapReport/||g;s|css/||g' results/qualimapReport.html > '/galaxy/server/database/objects/9/d/b/dataset_9db0550e-cc4f-47e4-8028-ab11ecf2b2d8.dat' && mkdir '/galaxy/server/database/objects/9/d/b/dataset_9db0550e-cc4f-47e4-8028-ab11ecf2b2d8_files' && mv results/css/*.css '/galaxy/server/database/objects/9/d/b/dataset_9db0550e-cc4f-47e4-8028-ab11ecf2b2d8_files' && mv results/css/*.png '/galaxy/server/database/objects/9/d/b/dataset_9db0550e-cc4f-47e4-8028-ab11ecf2b2d8_files' && if [ -d results/images_qualimapReport ]; then mv results/images_qualimapReport/* '/galaxy/server/database/objects/9/d/b/dataset_9db0550e-cc4f-47e4-8028-ab11ecf2b2d8_files' && for file in $(ls -A results/raw_data_qualimapReport); do mv \"results/raw_data_qualimapReport/$file\" `echo \"results/$file\" | sed 's/(//;s/)//'`; done fi && mv results/genome_results.txt results/summary_report.txt", "user_email": "tests@fake.org", "command_version": "2.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "plot_specific": "{\"genome_gc_distr\": null, \"homopolymer_size\": \"3\", \"n_bins\": \"400\", \"paint_chromosome_limits\": true}", "duplicate_skipping": "\"0\"", "per_base_coverage": "true", "stats_regions": "{\"__current_case__\": 0, \"region_select\": \"all\"}"}, "inputs": {"input1": {"id": "29d0911801055dab", "src": "hda", "uuid": "df12f0ab-0792-4bc0-892b-90760cc67a2e"}}, "outputs": {"raw_data|__part__|genome_results": {"id": "6e59bdb343696e5e", "src": "hda", "uuid": "9a2d7aed-092d-4804-bcb9-d397f218fedd"}, "raw_data|__part__|coverage_across_reference": {"id": "8608931a7cdc3273", "src": "hda", "uuid": "96eff902-851b-4e61-82d2-40019e30df3f"}, "raw_data|__part__|coverage_histogram": {"id": "9aec95a51008d2e1", "src": "hda", "uuid": "56ed1ef1-204a-4494-bb6b-12a4180ec665"}, "raw_data|__part__|genome_fraction_coverage": {"id": "c66acfb3e4ee5fa5", "src": "hda", "uuid": "c150482e-10a4-4117-9887-3fb70a4116a1"}, "raw_data|__part__|duplication_rate_histogram": {"id": "f4333311450069e1", "src": "hda", "uuid": "d88c2e68-6f25-4814-a890-66183a8ec1e9"}, "raw_data|__part__|homopolymer_indels": {"id": "3b7f688518dccb60", "src": "hda", "uuid": "d711fbe9-627f-41fe-8b9c-b0a7c657e21d"}, "raw_data|__part__|insert_size_across_reference": {"id": "f535695a4eeca412", "src": "hda", "uuid": "9df2647c-de01-473d-8d7d-e4e9947e1d6f"}, "raw_data|__part__|insert_size_histogram": {"id": "90747c5901aec4f1", "src": "hda", "uuid": "d71e7ce3-9d3e-4118-89e7-108402993e7e"}, "raw_data|__part__|mapped_reads_clipping_profile": {"id": "bf30c50aedb01f18", "src": "hda", "uuid": "5acf7e8f-6a27-4146-bfc8-f0c18d41db6e"}, "raw_data|__part__|mapped_reads_gc-content_distribution": {"id": "1617b56aab8d2d53", "src": "hda", "uuid": "81481884-f2a9-4850-b213-bf2372f41f6b"}, "raw_data|__part__|mapped_reads_nucleotide_content": {"id": "f93cc96a0035a39f", "src": "hda", "uuid": "7714093e-70c8-41a9-9aa7-e4cdd6ed7937"}, "raw_data|__part__|mapping_quality_across_reference": {"id": "c390362103cef5e9", "src": "hda", "uuid": "7ddcf173-0c50-4025-8df8-d5a368bc5d61"}, "raw_data|__part__|mapping_quality_histogram": {"id": "4c1637f2111138b3", "src": "hda", "uuid": "e2a109c6-dd16-4b9e-8f30-65b8a2e0fd02"}, "output_html": {"id": "84d1df44823d4243", "src": "hda", "uuid": "9db0550e-cc4f-47e4-8028-ab11ecf2b2d8"}, "output_per_base_coverage": {"id": "bf5627b8dab040b8", "src": "hda", "uuid": "e783cbbc-5e15-4a47-b41c-b52de419ccc5"}}, "copied_from_job_id": null, "output_collections": {"raw_data": {"src": "hdca", "id": "4a948b52e0692223"}}, "tool_stdout": "Java memory size is set to 1200M\nLaunching application...\n\ndetected environment java options -Djava.awt.headless=true -Xmx25769m\nQualiMap v.2.3\nBuilt on 2023-05-19 16:57\n\nSelected tool: bamqc\nAvailable memory (Mb): 389\nMax memory (Mb): 26121\nStarting bam qc....\nLoading sam header...\nLoading locator...\nLoading reference...\nOnly flagged duplicate alignments will be skipped...\nNumber of windows: 400, effective number of windows: 325\nChunk of reads size: 1000\nNumber of threads: 1\nProcessed 50 out of 325 windows...\nProcessed 100 out of 325 windows...\nProcessed 150 out of 325 windows...\nProcessed 200 out of 325 windows...\nProcessed 250 out of 325 windows...\nProcessed 300 out of 325 windows...\nTotal processed windows:325\nNumber of reads: 100\nNumber of valid reads: 100\nNumber of correct strand reads:0\n\nInside of regions...\nNum mapped reads: 100\nNum mapped first of pair: 0\nNum mapped second of pair: 0\nNum singletons: 0\nTime taken to analyze reads: 0\nComputing descriptors...\nnumberOfMappedBases: 12665\nreferenceSize: 650\nnumberOfSequencedBases: 7465\nnumberOfAs: 1910\nComputing per chromosome statistics...\nComputing histograms...\nOverall analysis time: 0\nend of bam qc\nComputing report...\nWriting HTML report...\nHTML report created successfully\n\nFinished\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Java memory size is set to 1200M\nLaunching application...\n\ndetected environment java options -Djava.awt.headless=true -Xmx25769m\nQualiMap v.2.3\nBuilt on 2023-05-19 16:57\n\nSelected tool: bamqc\nAvailable memory (Mb): 389\nMax memory (Mb): 26121\nStarting bam qc....\nLoading sam header...\nLoading locator...\nLoading reference...\nOnly flagged duplicate alignments will be skipped...\nNumber of windows: 400, effective number of windows: 325\nChunk of reads size: 1000\nNumber of threads: 1\nProcessed 50 out of 325 windows...\nProcessed 100 out of 325 windows...\nProcessed 150 out of 325 windows...\nProcessed 200 out of 325 windows...\nProcessed 250 out of 325 windows...\nProcessed 300 out of 325 windows...\nTotal processed windows:325\nNumber of reads: 100\nNumber of valid reads: 100\nNumber of correct strand reads:0\n\nInside of regions...\nNum mapped reads: 100\nNum mapped first of pair: 0\nNum mapped second of pair: 0\nNum singletons: 0\nTime taken to analyze reads: 0\nComputing descriptors...\nnumberOfMappedBases: 12665\nreferenceSize: 650\nnumberOfSequencedBases: 7465\nnumberOfAs: 1910\nComputing per chromosome statistics...\nComputing histograms...\nOverall analysis time: 0\nend of bam qc\nComputing report...\nWriting HTML report...\nHTML report created successfully\n\nFinished\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:50:58", "plugin": "core", "name": "end_epoch", "raw_value": "1727031058.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:50:53", "plugin": "core", "name": "start_epoch", "raw_value": "1727031053.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "qualimap_bamqc/2.3+galaxy0-2", "has_data": true, "data": {"tool_id": "qualimap_bamqc", "tool_version": "2.3+galaxy0", "test_index": 2, "time_seconds": 48.11313843727112, "inputs": {"input1": {"src": "hda", "id": "8e9738d7a25e86a8"}, "stats_regions|regions": {"src": "hda", "id": "64019a0d6a191c5c"}, "stats_regions|region_select": "custom_regions"}, "job": {"model_class": "Job", "id": "b39a57cfa0641e66", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:51:48.394064", "update_time": "2024-09-22T18:52:10.350885", "galaxy_version": "24.1", "external_id": "gxy-nbslr", "handler": null, "job_runner_name": null, "command_line": "export JAVA_OPTS=\"-Djava.awt.headless=true -Xmx${GALAXY_MEMORY_MB:-1024}m\" && ln -s '/galaxy/server/database/objects/7/4/7/dataset_747bdaea-4725-44a1-8b05-4a65a5b9acb6.dat' regions.gtf && ln -s '/galaxy/server/database/objects/7/4/4/dataset_74441475-a126-4687-bc0a-09484a0610b3.dat' 'test_mapped_reads_bam' && qualimap bamqc -bam 'test_mapped_reads_bam' -outdir results -outformat html --collect-overlap-pairs -gff regions.gtf -nw 400 --paint-chromosome-limits -hm 3 --skip-duplicated --skip-dup-mode 0 -nt ${GALAXY_SLOTS:-1} && sed 's|images_qualimapReport/||g;s|css/||g' results/qualimapReport.html > '/galaxy/server/database/objects/3/e/1/dataset_3e1cc151-110b-42ee-8c61-351248df9fc3.dat' && mkdir '/galaxy/server/database/objects/3/e/1/dataset_3e1cc151-110b-42ee-8c61-351248df9fc3_files' && mv results/css/*.css '/galaxy/server/database/objects/3/e/1/dataset_3e1cc151-110b-42ee-8c61-351248df9fc3_files' && mv results/css/*.png '/galaxy/server/database/objects/3/e/1/dataset_3e1cc151-110b-42ee-8c61-351248df9fc3_files' && if [ -d results/images_qualimapReport ]; then mv results/images_qualimapReport/* '/galaxy/server/database/objects/3/e/1/dataset_3e1cc151-110b-42ee-8c61-351248df9fc3_files' && for file in $(ls -A results/raw_data_qualimapReport); do mv \"results/raw_data_qualimapReport/$file\" `echo \"results/$file\" | sed 's/(//;s/)//'`; done fi && mv results/genome_results.txt results/summary_report.txt", "user_email": "tests@fake.org", "command_version": "2.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "plot_specific": "{\"genome_gc_distr\": null, \"homopolymer_size\": \"3\", \"n_bins\": \"400\", \"paint_chromosome_limits\": true}", "duplicate_skipping": "\"0\"", "per_base_coverage": "false", "stats_regions": "{\"__current_case__\": 1, \"outside_stats\": false, \"region_select\": \"custom_regions\", \"regions\": {\"values\": [{\"id\": 94, \"src\": \"hda\"}]}}"}, "inputs": {"input1": {"id": "8e9738d7a25e86a8", "src": "hda", "uuid": "74441475-a126-4687-bc0a-09484a0610b3"}, "stats_regions|regions": {"id": "64019a0d6a191c5c", "src": "hda", "uuid": "747bdaea-4725-44a1-8b05-4a65a5b9acb6"}}, "outputs": {"raw_data|__part__|genome_results": {"id": "cddfab12e1688665", "src": "hda", "uuid": "2af89ade-41c5-4b84-9efc-1600643e8741"}, "raw_data|__part__|coverage_across_reference": {"id": "ed94d7232d27f1a8", "src": "hda", "uuid": "96ccb919-8674-437d-872a-1c5dcb90bfe9"}, "raw_data|__part__|coverage_histogram": {"id": "05870a2022eff8bc", "src": "hda", "uuid": "c7762809-c715-4c1c-9e96-299c77f90a41"}, "raw_data|__part__|genome_fraction_coverage": {"id": "e041212b548a66e8", "src": "hda", "uuid": "e0ec3fe5-5718-40a0-8bc2-77f526e2921f"}, "raw_data|__part__|duplication_rate_histogram": {"id": "9b6728bb95418e81", "src": "hda", "uuid": "1f1f7e66-6e01-4fa4-bf65-ad474fffee64"}, "raw_data|__part__|homopolymer_indels": {"id": "97249fbef5624bb7", "src": "hda", "uuid": "59feb650-cb90-4af6-b609-3c1f8ff1c841"}, "raw_data|__part__|insert_size_across_reference": {"id": "6211649e9736ffb6", "src": "hda", "uuid": "5e5e20e7-b179-46e7-bfcf-c981d47d7335"}, "raw_data|__part__|insert_size_histogram": {"id": "1cf2b57e116100bf", "src": "hda", "uuid": "df0af9af-a2b8-4560-a37f-0f2dabe8016e"}, "raw_data|__part__|mapped_reads_clipping_profile": {"id": "55ed7c7ad1d2f76e", "src": "hda", "uuid": "d6c7db3d-ac80-48bd-ac0c-afa69f40fb04"}, "raw_data|__part__|mapped_reads_gc-content_distribution": {"id": "dfcffcdf8e4de4f3", "src": "hda", "uuid": "337ada50-7427-456b-be2c-7beae7f30588"}, "raw_data|__part__|mapped_reads_nucleotide_content": {"id": "65509f6dc4fc7fbd", "src": "hda", "uuid": "87c6719c-e93b-4a66-93be-490d91b54663"}, "raw_data|__part__|mapping_quality_across_reference": {"id": "24755ecc2498cdfd", "src": "hda", "uuid": "89e1c21f-b605-407d-bc1a-702df4d1f621"}, "raw_data|__part__|mapping_quality_histogram": {"id": "05576105d0636c9d", "src": "hda", "uuid": "cab1926f-bba8-46cb-b057-a650cf907c37"}, "output_html": {"id": "cee84bce56029b58", "src": "hda", "uuid": "3e1cc151-110b-42ee-8c61-351248df9fc3"}}, "copied_from_job_id": null, "output_collections": {"raw_data": {"src": "hdca", "id": "8cca6bebbdb3c85d"}}, "tool_stdout": "Java memory size is set to 1200M\nLaunching application...\n\ndetected environment java options -Djava.awt.headless=true -Xmx25769m\nQualiMap v.2.3\nBuilt on 2023-05-19 16:57\n\nSelected tool: bamqc\nAvailable memory (Mb): 389\nMax memory (Mb): 26121\nStarting bam qc....\nLoading sam header...\nLoading locator...\nLoading reference...\nOnly flagged duplicate alignments will be skipped...\nNumber of windows: 400, effective number of windows: 325\nChunk of reads size: 1000\nNumber of threads: 1\nInitializing regions from regions.gtf.....\nFound 4 regions\nFilling region references... \nProcessed 50 out of 325 windows...\nProcessed 100 out of 325 windows...\nProcessed 150 out of 325 windows...\nProcessed 200 out of 325 windows...\nProcessed 250 out of 325 windows...\nProcessed 300 out of 325 windows...\nTotal processed windows:325\nNumber of reads: 100\nNumber of valid reads: 100\nNumber of correct strand reads:0\n\nInside of regions...\nNum mapped reads: 82\nNum mapped first of pair: 0\nNum mapped second of pair: 0\nNum singletons: 0\nTime taken to analyze reads: 0\nComputing descriptors...\nnumberOfMappedBases: 6451\nreferenceSize: 650\nnumberOfSequencedBases: 5101\nnumberOfAs: 1243\nComputing per chromosome statistics...\nComputing histograms...\nOverall analysis time: 0\nend of bam qc\nComputing report...\nWriting HTML report...\nHTML report created successfully\n\nFinished\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Java memory size is set to 1200M\nLaunching application...\n\ndetected environment java options -Djava.awt.headless=true -Xmx25769m\nQualiMap v.2.3\nBuilt on 2023-05-19 16:57\n\nSelected tool: bamqc\nAvailable memory (Mb): 389\nMax memory (Mb): 26121\nStarting bam qc....\nLoading sam header...\nLoading locator...\nLoading reference...\nOnly flagged duplicate alignments will be skipped...\nNumber of windows: 400, effective number of windows: 325\nChunk of reads size: 1000\nNumber of threads: 1\nInitializing regions from regions.gtf.....\nFound 4 regions\nFilling region references... \nProcessed 50 out of 325 windows...\nProcessed 100 out of 325 windows...\nProcessed 150 out of 325 windows...\nProcessed 200 out of 325 windows...\nProcessed 250 out of 325 windows...\nProcessed 300 out of 325 windows...\nTotal processed windows:325\nNumber of reads: 100\nNumber of valid reads: 100\nNumber of correct strand reads:0\n\nInside of regions...\nNum mapped reads: 82\nNum mapped first of pair: 0\nNum mapped second of pair: 0\nNum singletons: 0\nTime taken to analyze reads: 0\nComputing descriptors...\nnumberOfMappedBases: 6451\nreferenceSize: 650\nnumberOfSequencedBases: 5101\nnumberOfAs: 1243\nComputing per chromosome statistics...\nComputing histograms...\nOverall analysis time: 0\nend of bam qc\nComputing report...\nWriting HTML report...\nHTML report created successfully\n\nFinished\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:51:55", "plugin": "core", "name": "end_epoch", "raw_value": "1727031115.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:51:50", "plugin": "core", "name": "start_epoch", "raw_value": "1727031110.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "qualimap_bamqc/2.3+galaxy0-3", "has_data": true, "data": {"tool_id": "qualimap_bamqc", "tool_version": "2.3+galaxy0", "test_index": 3, "time_seconds": 46.96489429473877, "inputs": {"input1": {"src": "hda", "id": "0261da2dfe29a82a"}, "stats_regions|regions": {"src": "hda", "id": "e4ac1ace7cb0990a"}, "stats_regions|region_select": "custom_regions", "per_base_coverage": true}, "job": {"model_class": "Job", "id": "24c429f3abbdf5b7", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:52:35.549456", "update_time": "2024-09-22T18:52:56.987787", "galaxy_version": "24.1", "external_id": "gxy-pkqw5", "handler": null, "job_runner_name": null, "command_line": "export JAVA_OPTS=\"-Djava.awt.headless=true -Xmx${GALAXY_MEMORY_MB:-1024}m\" && ln -s '/galaxy/server/database/objects/3/0/e/dataset_30eb5049-fae1-4cd8-99ab-1cac575f9271.dat' regions.gtf && ln -s '/galaxy/server/database/objects/c/1/f/dataset_c1f47842-088a-4279-85c0-6873ba229ee5.dat' 'test_mapped_reads_bam' && qualimap bamqc -bam 'test_mapped_reads_bam' -outdir results -outformat html --collect-overlap-pairs -gff regions.gtf --output-genome-coverage results/coverage.txt -nw 400 --paint-chromosome-limits -hm 3 --skip-duplicated --skip-dup-mode 0 -nt ${GALAXY_SLOTS:-1} && mv results/coverage.txt '/galaxy/server/database/objects/7/a/c/dataset_7acd7c6f-452d-45e4-91f2-209b997e7099.dat' && sed 's|images_qualimapReport/||g;s|css/||g' results/qualimapReport.html > '/galaxy/server/database/objects/9/1/3/dataset_913c6c55-e98b-4a3a-9fde-083602bbab6e.dat' && mkdir '/galaxy/server/database/objects/9/1/3/dataset_913c6c55-e98b-4a3a-9fde-083602bbab6e_files' && mv results/css/*.css '/galaxy/server/database/objects/9/1/3/dataset_913c6c55-e98b-4a3a-9fde-083602bbab6e_files' && mv results/css/*.png '/galaxy/server/database/objects/9/1/3/dataset_913c6c55-e98b-4a3a-9fde-083602bbab6e_files' && if [ -d results/images_qualimapReport ]; then mv results/images_qualimapReport/* '/galaxy/server/database/objects/9/1/3/dataset_913c6c55-e98b-4a3a-9fde-083602bbab6e_files' && for file in $(ls -A results/raw_data_qualimapReport); do mv \"results/raw_data_qualimapReport/$file\" `echo \"results/$file\" | sed 's/(//;s/)//'`; done fi && mv results/genome_results.txt results/summary_report.txt", "user_email": "tests@fake.org", "command_version": "2.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "plot_specific": "{\"genome_gc_distr\": null, \"homopolymer_size\": \"3\", \"n_bins\": \"400\", \"paint_chromosome_limits\": true}", "duplicate_skipping": "\"0\"", "per_base_coverage": "true", "stats_regions": "{\"__current_case__\": 1, \"outside_stats\": false, \"region_select\": \"custom_regions\", \"regions\": {\"values\": [{\"id\": 110, \"src\": \"hda\"}]}}"}, "inputs": {"input1": {"id": "0261da2dfe29a82a", "src": "hda", "uuid": "c1f47842-088a-4279-85c0-6873ba229ee5"}, "stats_regions|regions": {"id": "e4ac1ace7cb0990a", "src": "hda", "uuid": "30eb5049-fae1-4cd8-99ab-1cac575f9271"}}, "outputs": {"raw_data|__part__|genome_results": {"id": "0b2bd508b8904d58", "src": "hda", "uuid": "4555792a-6cc6-46b3-850a-831bf19ef738"}, "raw_data|__part__|coverage_across_reference": {"id": "755753a41550366c", "src": "hda", "uuid": "daae6922-80c7-47e0-9d41-fa6b94af6db2"}, "raw_data|__part__|coverage_histogram": {"id": "73bce02258136c59", "src": "hda", "uuid": "cb7a73a3-27c2-47ff-8b92-29ed07d1f59e"}, "raw_data|__part__|genome_fraction_coverage": {"id": "92e4a16636f870a1", "src": "hda", "uuid": "c09aac23-bcd9-49bc-8927-5d2ce8a86439"}, "raw_data|__part__|duplication_rate_histogram": {"id": "711d1c6a832e4812", "src": "hda", "uuid": "e858995f-263b-4839-aa0d-816ac3ca0318"}, "raw_data|__part__|homopolymer_indels": {"id": "7caf0227b06d2b6d", "src": "hda", "uuid": "e25dd321-8727-418a-a8a9-71afb4faa44c"}, "raw_data|__part__|insert_size_across_reference": {"id": "3893451f16a76961", "src": "hda", "uuid": "b7d49727-0621-4f6d-83d9-c159b5fce90d"}, "raw_data|__part__|insert_size_histogram": {"id": "257a1458dc621405", "src": "hda", "uuid": "c2b34b55-7e87-4881-a3ce-598cc79b15df"}, "raw_data|__part__|mapped_reads_clipping_profile": {"id": "1e1b7bbb50087229", "src": "hda", "uuid": "09bc2744-a447-410f-92d5-b5db573b566a"}, "raw_data|__part__|mapped_reads_gc-content_distribution": {"id": "a0d815711ed73e82", "src": "hda", "uuid": "5dc8840a-21aa-4667-9fd4-91ee931f17b3"}, "raw_data|__part__|mapped_reads_nucleotide_content": {"id": "31ba71a5468dd219", "src": "hda", "uuid": "61ead43e-9e69-4c14-896c-55773c3ef8ee"}, "raw_data|__part__|mapping_quality_across_reference": {"id": "6e5355263cf67873", "src": "hda", "uuid": "eaba31f0-2577-4c42-984c-0e2f05eb26c4"}, "raw_data|__part__|mapping_quality_histogram": {"id": "228875ce427a57fd", "src": "hda", "uuid": "5001b024-bd13-40b9-9a32-07cd93a863d8"}, "output_html": {"id": "13cdcdbe98abef25", "src": "hda", "uuid": "913c6c55-e98b-4a3a-9fde-083602bbab6e"}, "output_per_base_coverage": {"id": "e8b7c9916a5502ab", "src": "hda", "uuid": "7acd7c6f-452d-45e4-91f2-209b997e7099"}}, "copied_from_job_id": null, "output_collections": {"raw_data": {"src": "hdca", "id": "2e8868accb6d4635"}}, "tool_stdout": "Java memory size is set to 1200M\nLaunching application...\n\ndetected environment java options -Djava.awt.headless=true -Xmx25769m\nQualiMap v.2.3\nBuilt on 2023-05-19 16:57\n\nSelected tool: bamqc\nAvailable memory (Mb): 389\nMax memory (Mb): 26121\nStarting bam qc....\nLoading sam header...\nLoading locator...\nLoading reference...\nOnly flagged duplicate alignments will be skipped...\nNumber of windows: 400, effective number of windows: 325\nChunk of reads size: 1000\nNumber of threads: 1\nInitializing regions from regions.gtf.....\nFound 4 regions\nFilling region references... \nProcessed 50 out of 325 windows...\nProcessed 100 out of 325 windows...\nProcessed 150 out of 325 windows...\nProcessed 200 out of 325 windows...\nProcessed 250 out of 325 windows...\nProcessed 300 out of 325 windows...\nTotal processed windows:325\nNumber of reads: 100\nNumber of valid reads: 100\nNumber of correct strand reads:0\n\nInside of regions...\nNum mapped reads: 82\nNum mapped first of pair: 0\nNum mapped second of pair: 0\nNum singletons: 0\nTime taken to analyze reads: 0\nComputing descriptors...\nnumberOfMappedBases: 6451\nreferenceSize: 650\nnumberOfSequencedBases: 5101\nnumberOfAs: 1243\nComputing per chromosome statistics...\nComputing histograms...\nOverall analysis time: 0\nend of bam qc\nComputing report...\nWriting HTML report...\nHTML report created successfully\n\nFinished\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Java memory size is set to 1200M\nLaunching application...\n\ndetected environment java options -Djava.awt.headless=true -Xmx25769m\nQualiMap v.2.3\nBuilt on 2023-05-19 16:57\n\nSelected tool: bamqc\nAvailable memory (Mb): 389\nMax memory (Mb): 26121\nStarting bam qc....\nLoading sam header...\nLoading locator...\nLoading reference...\nOnly flagged duplicate alignments will be skipped...\nNumber of windows: 400, effective number of windows: 325\nChunk of reads size: 1000\nNumber of threads: 1\nInitializing regions from regions.gtf.....\nFound 4 regions\nFilling region references... \nProcessed 50 out of 325 windows...\nProcessed 100 out of 325 windows...\nProcessed 150 out of 325 windows...\nProcessed 200 out of 325 windows...\nProcessed 250 out of 325 windows...\nProcessed 300 out of 325 windows...\nTotal processed windows:325\nNumber of reads: 100\nNumber of valid reads: 100\nNumber of correct strand reads:0\n\nInside of regions...\nNum mapped reads: 82\nNum mapped first of pair: 0\nNum mapped second of pair: 0\nNum singletons: 0\nTime taken to analyze reads: 0\nComputing descriptors...\nnumberOfMappedBases: 6451\nreferenceSize: 650\nnumberOfSequencedBases: 5101\nnumberOfAs: 1243\nComputing per chromosome statistics...\nComputing histograms...\nOverall analysis time: 0\nend of bam qc\nComputing report...\nWriting HTML report...\nHTML report created successfully\n\nFinished\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:52:42", "plugin": "core", "name": "end_epoch", "raw_value": "1727031162.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:52:38", "plugin": "core", "name": "start_epoch", "raw_value": "1727031158.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "qualimap_bamqc/2.3+galaxy0-4", "has_data": true, "data": {"tool_id": "qualimap_bamqc", "tool_version": "2.3+galaxy0", "test_index": 4, "time_seconds": 48.58277344703674, "inputs": {"input1": {"src": "hda", "id": "2659c783a61b04b5"}, "stats_regions|regions": {"src": "hda", "id": "a627cd48f111ee3e"}, "stats_regions|outside_stats": true, "stats_regions|region_select": "custom_regions", "per_base_coverage": true}, "job": {"model_class": "Job", "id": "66c8b670a8d53b88", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:53:23.622652", "update_time": "2024-09-22T18:53:45.567316", "galaxy_version": "24.1", "external_id": "gxy-sz89h", "handler": null, "job_runner_name": null, "command_line": "export JAVA_OPTS=\"-Djava.awt.headless=true -Xmx${GALAXY_MEMORY_MB:-1024}m\" && ln -s '/galaxy/server/database/objects/d/b/3/dataset_db3d2bf2-c185-4dc9-bde3-22debb6deba1.dat' regions.gtf && ln -s '/galaxy/server/database/objects/1/f/d/dataset_1fd4f7de-d806-4b71-bca8-7fecb6013cb9.dat' 'test_mapped_reads_bam' && qualimap bamqc -bam 'test_mapped_reads_bam' -outdir results -outformat html --collect-overlap-pairs -gff regions.gtf --outside-stats --output-genome-coverage /dev/null -nw 400 --paint-chromosome-limits -hm 3 --skip-duplicated --skip-dup-mode 0 -nt ${GALAXY_SLOTS:-1} && mv results/outside_coverage.txt '/galaxy/server/database/objects/8/d/8/dataset_8d8a5cfc-cca2-41c8-9258-e9a16854080d.dat' && sed 's|images_qualimapReportOutsideRegions/||g;s|css/||g' results/qualimapReportOutsideRegions.html > '/galaxy/server/database/objects/d/0/6/dataset_d066d640-d6ed-4e76-8dbe-bc87434d1899.dat' && mkdir '/galaxy/server/database/objects/d/0/6/dataset_d066d640-d6ed-4e76-8dbe-bc87434d1899_files' && mv results/css/*.css '/galaxy/server/database/objects/d/0/6/dataset_d066d640-d6ed-4e76-8dbe-bc87434d1899_files' && mv results/css/*.png '/galaxy/server/database/objects/d/0/6/dataset_d066d640-d6ed-4e76-8dbe-bc87434d1899_files' && if [ -d results/images_qualimapReportOutsideRegions ]; then mv results/images_qualimapReportOutsideRegions/* '/galaxy/server/database/objects/d/0/6/dataset_d066d640-d6ed-4e76-8dbe-bc87434d1899_files' && for file in $(ls -A results/raw_data_qualimapReportOutsideRegions); do mv \"results/raw_data_qualimapReportOutsideRegions/$file\" `echo \"results/$file\" | sed 's/(//;s/)//'`; done fi && mv results/outside_results.txt results/summary_report.txt", "user_email": "tests@fake.org", "command_version": "2.3", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "plot_specific": "{\"genome_gc_distr\": null, \"homopolymer_size\": \"3\", \"n_bins\": \"400\", \"paint_chromosome_limits\": true}", "duplicate_skipping": "\"0\"", "per_base_coverage": "true", "stats_regions": "{\"__current_case__\": 1, \"outside_stats\": true, \"region_select\": \"custom_regions\", \"regions\": {\"values\": [{\"id\": 127, \"src\": \"hda\"}]}}"}, "inputs": {"input1": {"id": "2659c783a61b04b5", "src": "hda", "uuid": "1fd4f7de-d806-4b71-bca8-7fecb6013cb9"}, "stats_regions|regions": {"id": "a627cd48f111ee3e", "src": "hda", "uuid": "db3d2bf2-c185-4dc9-bde3-22debb6deba1"}}, "outputs": {"raw_data|__part__|genome_results": {"id": "c7c9bd45055a66e2", "src": "hda", "uuid": "8a5d4355-1960-4bb6-aecf-6b48879a4bda"}, "raw_data|__part__|coverage_across_reference": {"id": "f1ba1165aac2478e", "src": "hda", "uuid": "dec717c5-412d-4f53-83b5-4c3498615638"}, "raw_data|__part__|coverage_histogram": {"id": "67f4878618a03e81", "src": "hda", "uuid": "b88ad497-0088-422d-80ef-cb06d7c6ee9b"}, "raw_data|__part__|genome_fraction_coverage": {"id": "8e3cd42fade67d71", "src": "hda", "uuid": "04fa3ce4-33c6-4ecc-9123-8924522969b1"}, "raw_data|__part__|duplication_rate_histogram": {"id": "87f1dec4b968275c", "src": "hda", "uuid": "13f0174f-c2e4-480f-8946-2f4492148f35"}, "raw_data|__part__|homopolymer_indels": {"id": "68822d38a18be506", "src": "hda", "uuid": "130549ed-dce2-43e2-8402-60026ecdde3f"}, "raw_data|__part__|insert_size_across_reference": {"id": "38f756a732f89588", "src": "hda", "uuid": "9507f90e-ff3f-456b-8656-d355f17a0f1b"}, "raw_data|__part__|insert_size_histogram": {"id": "50cb20a192d153eb", "src": "hda", "uuid": "2095aec4-f365-4435-8528-e1f3b9e96dae"}, "raw_data|__part__|mapped_reads_clipping_profile": {"id": "6fab46106d565c01", "src": "hda", "uuid": "64f75b52-6798-41bd-849c-8716cb5ad26e"}, "raw_data|__part__|mapped_reads_gc-content_distribution": {"id": "24371a49dc8408da", "src": "hda", "uuid": "74cd79a4-3839-467d-9858-3f2a4b966b45"}, "raw_data|__part__|mapped_reads_nucleotide_content": {"id": "6409a12dbea93ff2", "src": "hda", "uuid": "464d1e5a-0936-4d39-bb4f-f51d923715c1"}, 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will be skipped...\nNumber of windows: 400, effective number of windows: 325\nChunk of reads size: 1000\nNumber of threads: 1\nInitializing regions from regions.gtf.....\nFound 4 regions\nFilling region references... \nProcessed 50 out of 325 windows...\nProcessed 100 out of 325 windows...\nProcessed 150 out of 325 windows...\nProcessed 200 out of 325 windows...\nProcessed 250 out of 325 windows...\nProcessed 300 out of 325 windows...\nTotal processed windows:325\nNumber of reads: 100\nNumber of valid reads: 100\nNumber of correct strand reads:0\n\nInside of regions...\nNum mapped reads: 82\nNum mapped first of pair: 0\nNum mapped second of pair: 0\nNum singletons: 0\n\nOuside of regions...\nNum mapped reads: 18\nNum mapped first of pair: 0\nNum mapped second of pair: 0\nNum singletons: 0\nTime taken to analyze reads: 0\nComputing descriptors...\nnumberOfMappedBases: 6451\nreferenceSize: 650\nnumberOfSequencedBases: 5101\nnumberOfAs: 1243\nComputing per chromosome statistics...\nComputing histograms...\nComputing descriptors for outside regions...\nnumberOfMappedBases: 6214\nreferenceSize: 650\nnumberOfSequencedBases: 2364\nnumberOfAs: 667\nComputing per chromosome statistics for outside regions...\nComputing histograms for outside regions...\nOverall analysis time: 0\nend of bam qc\nComputing report...\nWriting HTML report...\nHTML report created successfully\n\nFinished\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "Java memory size is set to 1200M\nLaunching application...\n\ndetected environment java options -Djava.awt.headless=true -Xmx25769m\nQualiMap v.2.3\nBuilt on 2023-05-19 16:57\n\nSelected tool: bamqc\nAvailable memory (Mb): 389\nMax memory (Mb): 26121\nStarting bam qc....\nLoading sam header...\nLoading locator...\nLoading reference...\nOnly flagged duplicate alignments will be skipped...\nNumber of windows: 400, effective number of windows: 325\nChunk of reads size: 1000\nNumber of threads: 1\nInitializing regions from regions.gtf.....\nFound 4 regions\nFilling region references... \nProcessed 50 out of 325 windows...\nProcessed 100 out of 325 windows...\nProcessed 150 out of 325 windows...\nProcessed 200 out of 325 windows...\nProcessed 250 out of 325 windows...\nProcessed 300 out of 325 windows...\nTotal processed windows:325\nNumber of reads: 100\nNumber of valid reads: 100\nNumber of correct strand reads:0\n\nInside of regions...\nNum mapped reads: 82\nNum mapped first of pair: 0\nNum mapped second of pair: 0\nNum singletons: 0\n\nOuside of regions...\nNum mapped reads: 18\nNum mapped first of pair: 0\nNum mapped second of pair: 0\nNum singletons: 0\nTime taken to analyze reads: 0\nComputing descriptors...\nnumberOfMappedBases: 6451\nreferenceSize: 650\nnumberOfSequencedBases: 5101\nnumberOfAs: 1243\nComputing per chromosome statistics...\nComputing histograms...\nComputing descriptors for outside regions...\nnumberOfMappedBases: 6214\nreferenceSize: 650\nnumberOfSequencedBases: 2364\nnumberOfAs: 667\nComputing per chromosome statistics for outside regions...\nComputing histograms for outside regions...\nOverall analysis time: 0\nend of bam qc\nComputing report...\nWriting HTML report...\nHTML report created successfully\n\nFinished\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "6 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "6.0000000"}, {"title": "Job End Time", "value": "2024-09-22 18:53:31", "plugin": "core", "name": "end_epoch", "raw_value": "1727031211.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:53:25", "plugin": "core", "name": "start_epoch", "raw_value": "1727031205.0000000"}, {"title": "Memory Allocated (MB)", "value": "25769", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "25769.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": 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ln -s '/galaxy/server/database/objects/6/f/2/dataset_6f265b4a-ccc0-4eca-a566-a81e3d9da4e9.dat' infile && reffa=\"reference.fa\" && ln -s '/galaxy/server/database/objects/d/a/6/dataset_da64ea74-091b-46e0-9e9b-2de5eb122a42.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools stats --ref-seq \"$reffa\" -@ $addthreads infile > '/galaxy/server/database/objects/5/e/e/dataset_5ee088a0-1d74-4ff3-8e18-c58e5aca1edd.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 0, \"select_region\": \"no\"}", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 186, \"src\": \"hda\"}]}}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "18ce24bae044c619", "src": "hda", "uuid": "6f265b4a-ccc0-4eca-a566-a81e3d9da4e9"}, "addref_cond|ref": {"id": "c5b5d01ee754942c", "src": "hda", "uuid": "da64ea74-091b-46e0-9e9b-2de5eb122a42"}}, "outputs": {"output": {"id": "672228a56bae35c2", "src": "hda", "uuid": "5ee088a0-1d74-4ff3-8e18-c58e5aca1edd"}}, "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": "2024-09-22 19:03:52", "plugin": "core", "name": "end_epoch", "raw_value": "1727031832.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:03:52", "plugin": "core", "name": "start_epoch", "raw_value": "1727031832.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-10", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 10, "time_seconds": 44.689982175827026, "inputs": {"input": {"src": "hda", "id": "d18b8080e14f39b3"}, "addref_cond|addref_select": "no", "cond_region|targetregions": {"src": "hda", "id": "90d0613a52964397"}, "cond_region|select_region": "tab", "remove_overlaps": true}, "job": {"model_class": "Job", "id": "ed94d7232d27f1a8", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:01:03.183029", "update_time": "2024-09-22T19:01:20.833914", "galaxy_version": "24.1", "external_id": "gxy-gx7vv", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/6/e/2/dataset_6e2d0817-388e-4b6e-ad25-89693868fcb4.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/9/6/2/metadata_962d1252-606a-42f9-ae4c-7f127cc6a21f.dat' infile.bai && samtools stats -t '/galaxy/server/database/objects/5/b/b/dataset_5bb5b71b-c732-434f-9af1-0e853d8aecf6.dat' -p -@ $addthreads infile > '/galaxy/server/database/objects/1/7/6/dataset_1769bbd7-5a3c-4913-b9d4-d0342b939e9c.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "true", "sparse": "false", "cond_region": "{\"__current_case__\": 2, \"select_region\": \"tab\", \"targetregions\": {\"values\": [{\"id\": 172, \"src\": \"hda\"}]}}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "d18b8080e14f39b3", "src": "hda", "uuid": "6e2d0817-388e-4b6e-ad25-89693868fcb4"}, "cond_region|targetregions": {"id": "90d0613a52964397", "src": "hda", "uuid": "5bb5b71b-c732-434f-9af1-0e853d8aecf6"}}, "outputs": {"output": {"id": "5595cb07e7491dd7", "src": "hda", "uuid": "1769bbd7-5a3c-4913-b9d4-d0342b939e9c"}}, "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": "2024-09-22 19:01:05", "plugin": "core", "name": "end_epoch", "raw_value": "1727031665.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:01:05", "plugin": "core", "name": "start_epoch", "raw_value": "1727031665.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-10", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 10, "time_seconds": 41.15989351272583, "inputs": {"input": {"src": "hda", "id": "79b79e39004a28b8"}, "addref_cond|addref_select": "no", "cond_region|targetregions": {"src": "hda", "id": "e0b6f6a52350c93e"}, "cond_region|select_region": "tab", "remove_overlaps": true}, "job": {"model_class": "Job", "id": "68822d38a18be506", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:09:58.256221", "update_time": "2024-09-22T19:10:13.896898", "galaxy_version": "24.1", "external_id": "gxy-hpbph", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/9/8/3/dataset_98367705-99a4-4307-89a7-31d96330f9d0.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/d/8/c/metadata_d8c492e0-71cf-48e4-9068-855e8e7d691a.dat' infile.bai && samtools stats -t '/galaxy/server/database/objects/b/c/b/dataset_bcb6865b-5209-4fb3-9c99-d97f8e0c37f5.dat' -p -@ $addthreads infile > '/galaxy/server/database/objects/1/3/7/dataset_137ef1de-007a-455f-9378-5022007c367f.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "true", "sparse": "false", "cond_region": "{\"__current_case__\": 2, \"select_region\": \"tab\", \"targetregions\": {\"values\": [{\"id\": 211, \"src\": \"hda\"}]}}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "79b79e39004a28b8", "src": "hda", "uuid": "98367705-99a4-4307-89a7-31d96330f9d0"}, "cond_region|targetregions": {"id": "e0b6f6a52350c93e", "src": "hda", "uuid": "bcb6865b-5209-4fb3-9c99-d97f8e0c37f5"}}, "outputs": {"output": {"id": "3497a43a628aa539", "src": "hda", "uuid": "137ef1de-007a-455f-9378-5022007c367f"}}, "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": "2024-09-22 19:10:00", "plugin": "core", "name": "end_epoch", "raw_value": "1727032200.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:10:00", "plugin": "core", "name": "start_epoch", "raw_value": "1727032200.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-11", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 11, "time_seconds": 41.420472621917725, "inputs": {"input": {"src": "hda", "id": "a8b2ceb9efb9e894"}, "addref_cond|ref": {"src": "hda", "id": "2f925a76a0742f8a"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "9b6728bb95418e81", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:01:46.748434", "update_time": "2024-09-22T19:02:02.541366", "galaxy_version": "24.1", "external_id": "gxy-lnzfp", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/5/4/6/dataset_546afebb-91d4-413c-aa44-44b4cf9b7aa2.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/1/3/5/metadata_13518ba9-9885-480a-9423-14dbdfbbb340.dat' infile.bai && reffa=\"reference.fa\" && ln -s '/galaxy/server/database/objects/5/7/7/dataset_5772826c-c638-4f52-a1cf-bc6660090ee4.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools stats --ref-seq \"$reffa\" -@ $addthreads infile > '/galaxy/server/database/objects/6/c/0/dataset_6c06ceb3-23fd-4ebf-8258-e733b4b97561.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 0, \"select_region\": \"no\"}", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 175, \"src\": \"hda\"}]}}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "a8b2ceb9efb9e894", "src": "hda", "uuid": "546afebb-91d4-413c-aa44-44b4cf9b7aa2"}, "addref_cond|ref": {"id": "2f925a76a0742f8a", "src": "hda", "uuid": "5772826c-c638-4f52-a1cf-bc6660090ee4"}}, "outputs": {"output": {"id": "311c79364e89d97c", "src": "hda", "uuid": "6c06ceb3-23fd-4ebf-8258-e733b4b97561"}}, "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": "2024-09-22 19:01:48", "plugin": "core", "name": "end_epoch", "raw_value": "1727031708.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:01:48", "plugin": "core", "name": "start_epoch", "raw_value": "1727031708.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-11", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 11, "time_seconds": 40.3206090927124, "inputs": {"input": {"src": "hda", "id": "3f96f37bdde89dc8"}, "addref_cond|ref": {"src": "hda", "id": "55702ef40a7a761e"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "6fab46106d565c01", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:10:38.968806", "update_time": "2024-09-22T19:10:54.246758", "galaxy_version": "24.1", "external_id": "gxy-65726", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/9/8/d/dataset_98d6f492-989f-461f-8ed9-c6f1776c28e3.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/f/2/6/metadata_f269ecf5-3ede-4414-b2e3-99aa277efa97.dat' infile.bai && reffa=\"reference.fa\" && ln -s '/galaxy/server/database/objects/4/7/d/dataset_47d97a36-dd50-45aa-94ec-fb585fb324ea.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools stats --ref-seq \"$reffa\" -@ $addthreads infile > '/galaxy/server/database/objects/e/8/8/dataset_e88959f3-a14a-4272-9fd6-91f25215cea7.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 0, \"select_region\": \"no\"}", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 214, \"src\": \"hda\"}]}}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "3f96f37bdde89dc8", "src": "hda", "uuid": "98d6f492-989f-461f-8ed9-c6f1776c28e3"}, "addref_cond|ref": {"id": "55702ef40a7a761e", "src": "hda", "uuid": "47d97a36-dd50-45aa-94ec-fb585fb324ea"}}, "outputs": {"output": {"id": "9d6fd47a87947a5a", "src": "hda", "uuid": "e88959f3-a14a-4272-9fd6-91f25215cea7"}}, "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": "2024-09-22 19:10:40", "plugin": "core", "name": "end_epoch", "raw_value": "1727032240.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:10:40", "plugin": "core", "name": "start_epoch", "raw_value": "1727032240.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-12", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 12, "time_seconds": 42.502402544021606, "inputs": {"input": {"src": "hda", "id": "1ac46435ea78d248"}, "split_output_cond|generate_tables": ["SN", "MPC", "GCC"], "split_output_cond|split_output_selector": "yes", "addref_cond|ref": {"src": "hda", "id": "a28a75871b82f3c6"}, "addref_cond|addref_select": "history"}, "job": {"model_class": "Job", "id": "1cf2b57e116100bf", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:02:28.084764", "update_time": "2024-09-22T19:02:44.532238", "galaxy_version": "24.1", "external_id": "gxy-5jjfg", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/3/6/f/dataset_36f1e2c0-2015-4d0b-8726-91025844b256.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/8/9/5/metadata_895a214b-921d-498b-a2bf-d6eff08a52fa.dat' infile.bai && reffa=\"reference.fa\" && ln -s '/galaxy/server/database/objects/b/c/7/dataset_bc79020a-f3f4-4c4f-87ac-dfba8edd81bf.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools stats --ref-seq \"$reffa\" -@ $addthreads infile > 'XXXX' && mkdir split && name=`cat 'XXXX' | grep '\\^SN' | cut -d'.' -f 1 | sed 's/^# //'` && awk '/\\^/{out=0} /\\^SN/{out=1} {if(out==1){print $0}}' 'XXXX' | sed 's/Use `grep .*` to extract this part.//' | sed 's/SN\\t//' > \"split/$name.tab\" && name=`cat 'XXXX' | grep '\\^MPC' | cut -d'.' -f 1 | sed 's/^# //'` && awk '/\\^/{out=0} /\\^MPC/{out=1} {if(out==1){print $0}}' 'XXXX' | sed 's/Use `grep .*` to extract this part.//' | sed 's/MPC\\t//' > \"split/$name.tab\" && name=`cat 'XXXX' | grep '\\^GCC' | cut -d'.' -f 1 | sed 's/^# //'` && awk '/\\^/{out=0} /\\^GCC/{out=1} {if(out==1){print $0}}' 'XXXX' | sed 's/Use `grep .*` to extract this part.//' | sed 's/GCC\\t//' > \"split/$name.tab\"", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 0, \"select_region\": \"no\"}", "addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 178, \"src\": 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"success"}}, {"id": "samtools_stats/2.0.5-3", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 3, "time_seconds": 41.32756781578064, "inputs": {"input": {"src": "hda", "id": "086d8c7a975b8162"}, "addref_cond|addref_select": "no", "cond_region|targetregions": {"src": "hda", "id": "3ae329f523d924dd"}, "cond_region|select_region": "tab"}, "job": {"model_class": "Job", "id": "92e4a16636f870a1", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:05:12.765756", "update_time": "2024-09-22T19:05:28.820893", "galaxy_version": "24.1", "external_id": "gxy-tlsc9", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/1/0/6/dataset_10688de6-7d2e-438d-af99-55dada90d5d6.dat' infile && samtools stats -t '/galaxy/server/database/objects/b/6/2/dataset_b6229e99-c028-4925-bc0a-ed62b77bb1a8.dat' -@ $addthreads infile > '/galaxy/server/database/objects/d/0/9/dataset_d090d04b-966c-4a5f-b018-d5ab3680ec37.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 2, \"select_region\": \"tab\", \"targetregions\": {\"values\": [{\"id\": 192, \"src\": \"hda\"}]}}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "086d8c7a975b8162", "src": "hda", "uuid": "10688de6-7d2e-438d-af99-55dada90d5d6"}, "cond_region|targetregions": {"id": "3ae329f523d924dd", "src": "hda", "uuid": "b6229e99-c028-4925-bc0a-ed62b77bb1a8"}}, "outputs": {"output": {"id": "4a4c437003421748", "src": "hda", "uuid": "d090d04b-966c-4a5f-b018-d5ab3680ec37"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Barcodes with tag BC differ in length at sequence 'ref1_grp1_p002'\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Barcodes with tag BC differ in length at sequence 'ref1_grp1_p002'\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": "2024-09-22 19:05:15", "plugin": "core", "name": "end_epoch", "raw_value": "1727031915.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:05:14", "plugin": "core", "name": "start_epoch", "raw_value": "1727031914.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-4", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 4, "time_seconds": 41.112889766693115, "inputs": {"input": {"src": "hda", "id": "02f38e9397fe15a2"}, "addref_cond|addref_select": "no", "cond_region|regions_repeat_0|region": "ref1:10-24", "cond_region|regions_repeat_1|region": "ref1:30-46", "cond_region|regions_repeat_2|region": "ref1:39-56", "cond_region|select_region": "text"}, "job": {"model_class": "Job", "id": "8608931a7cdc3273", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:56:55.101069", "update_time": "2024-09-22T18:57:10.861153", "galaxy_version": "24.1", "external_id": "gxy-n55s8", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/b/7/5/dataset_b755accf-84eb-4dd7-a201-75b853cae0a4.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/f/0/e/metadata_f0e40175-be96-4cad-be91-caada4c364f0.dat' infile.bai && samtools stats -@ $addthreads infile 'ref1:10-24' 'ref1:30-46' 'ref1:39-56' > '/galaxy/server/database/objects/e/0/c/dataset_e0c7b2d3-87f8-4a48-bee3-1e1aa2553831.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 1, \"regions_repeat\": [{\"__index__\": 0, \"region\": \"ref1:10-24\"}, {\"__index__\": 1, \"region\": \"ref1:30-46\"}, {\"__index__\": 2, \"region\": \"ref1:39-56\"}], \"select_region\": \"text\"}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "02f38e9397fe15a2", "src": "hda", "uuid": "b755accf-84eb-4dd7-a201-75b853cae0a4"}}, "outputs": {"output": {"id": "5fc19491eaefd6a0", "src": "hda", "uuid": "e0c7b2d3-87f8-4a48-bee3-1e1aa2553831"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Barcodes with tag BC differ in length at sequence 'ref1_grp1_p002'\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Barcodes with tag BC differ in length at sequence 'ref1_grp1_p002'\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": "2024-09-22 18:56:57", "plugin": "core", "name": "end_epoch", "raw_value": "1727031417.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:56:57", "plugin": "core", "name": "start_epoch", "raw_value": "1727031417.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-4", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 4, "time_seconds": 39.40816330909729, "inputs": {"input": {"src": "hda", "id": "08129bff60830b9f"}, "addref_cond|addref_select": "no", "cond_region|regions_repeat_0|region": "ref1:10-24", "cond_region|regions_repeat_1|region": "ref1:30-46", "cond_region|regions_repeat_2|region": "ref1:39-56", "cond_region|select_region": "text"}, "job": {"model_class": "Job", "id": "7caf0227b06d2b6d", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:05:52.303911", "update_time": "2024-09-22T19:06:08.093569", "galaxy_version": "24.1", "external_id": "gxy-pm7pq", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/2/a/d/dataset_2ad6d1c1-d6e2-4ccc-8365-3df804cfcbb4.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/a/6/0/metadata_a600b283-697b-4624-8261-05a904f71956.dat' infile.bai && samtools stats -@ $addthreads infile 'ref1:10-24' 'ref1:30-46' 'ref1:39-56' > '/galaxy/server/database/objects/2/7/8/dataset_278f83bf-ac8d-492d-8e02-4f5d3f618efc.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 1, \"regions_repeat\": [{\"__index__\": 0, \"region\": \"ref1:10-24\"}, {\"__index__\": 1, \"region\": \"ref1:30-46\"}, {\"__index__\": 2, \"region\": \"ref1:39-56\"}], \"select_region\": \"text\"}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "08129bff60830b9f", "src": "hda", "uuid": "2ad6d1c1-d6e2-4ccc-8365-3df804cfcbb4"}}, "outputs": {"output": {"id": "a6fe0632b4051f26", "src": "hda", "uuid": "278f83bf-ac8d-492d-8e02-4f5d3f618efc"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Barcodes with tag BC differ in length at sequence 'ref1_grp1_p002'\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Barcodes with tag BC differ in length at sequence 'ref1_grp1_p002'\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": "2024-09-22 19:05:54", "plugin": "core", "name": "end_epoch", "raw_value": "1727031954.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:05:54", "plugin": "core", "name": "start_epoch", "raw_value": "1727031954.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-5", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 5, "time_seconds": 40.87939405441284, "inputs": {"input": {"src": "hda", "id": "00bf5e33f5f60a84"}, "addref_cond|addref_select": "no", "cond_region|targetregions": {"src": "hda", "id": "cd988844606043bf"}, "cond_region|select_region": "tab", "cov_threshold": "4"}, "job": {"model_class": "Job", "id": "f4333311450069e1", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:57:35.364730", "update_time": "2024-09-22T18:57:51.606008", "galaxy_version": "24.1", "external_id": "gxy-h5mjl", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/5/6/2/dataset_5624f23a-9acd-4b74-bc9c-de20c23ae016.dat' infile && samtools stats -t '/galaxy/server/database/objects/0/4/f/dataset_04f16fe4-b7df-4a33-8f6e-9fbf18205a83.dat' -g 4 -@ $addthreads infile > '/galaxy/server/database/objects/f/3/8/dataset_f3831582-d8b9-45d1-b8ee-09fe4ba7c79c.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"4\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 2, \"select_region\": \"tab\", \"targetregions\": {\"values\": [{\"id\": 158, \"src\": \"hda\"}]}}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "00bf5e33f5f60a84", "src": "hda", "uuid": "5624f23a-9acd-4b74-bc9c-de20c23ae016"}, "cond_region|targetregions": {"id": "cd988844606043bf", "src": "hda", "uuid": "04f16fe4-b7df-4a33-8f6e-9fbf18205a83"}}, "outputs": {"output": {"id": "400fd7205f084227", "src": "hda", "uuid": "f3831582-d8b9-45d1-b8ee-09fe4ba7c79c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Barcodes with tag BC differ in length at sequence 'ref1_grp1_p002'\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Barcodes with tag BC differ in length at sequence 'ref1_grp1_p002'\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": "2024-09-22 18:57:37", "plugin": "core", "name": "end_epoch", "raw_value": "1727031457.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:57:37", "plugin": "core", "name": "start_epoch", "raw_value": "1727031457.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-5", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 5, "time_seconds": 40.34321069717407, "inputs": {"input": {"src": "hda", "id": "4df9a0e9bf061626"}, "addref_cond|addref_select": "no", "cond_region|targetregions": {"src": "hda", "id": "23fa96fce5eed89f"}, "cond_region|select_region": "tab", "cov_threshold": "4"}, "job": {"model_class": "Job", "id": "1e1b7bbb50087229", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:06:33.579596", "update_time": "2024-09-22T19:06:48.710240", "galaxy_version": "24.1", "external_id": "gxy-xpx92", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/2/d/3/dataset_2d39564f-1614-4f5b-b7ea-8a5fd2b74c62.dat' infile && samtools stats -t '/galaxy/server/database/objects/c/7/1/dataset_c71d1980-a561-4643-b853-4d9c5400a4f8.dat' -g 4 -@ $addthreads infile > '/galaxy/server/database/objects/b/f/f/dataset_bff954d4-e41a-4cfa-aa8d-165041606532.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"4\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 2, \"select_region\": \"tab\", \"targetregions\": {\"values\": [{\"id\": 197, \"src\": \"hda\"}]}}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "4df9a0e9bf061626", "src": "hda", "uuid": "2d39564f-1614-4f5b-b7ea-8a5fd2b74c62"}, "cond_region|targetregions": {"id": "23fa96fce5eed89f", "src": "hda", "uuid": "c71d1980-a561-4643-b853-4d9c5400a4f8"}}, "outputs": {"output": {"id": "536e88f8bbda2931", "src": "hda", "uuid": "bff954d4-e41a-4cfa-aa8d-165041606532"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Barcodes with tag BC differ in length at sequence 'ref1_grp1_p002'\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Barcodes with tag BC differ in length at sequence 'ref1_grp1_p002'\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": "2024-09-22 19:06:35", "plugin": "core", "name": "end_epoch", "raw_value": "1727031995.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:06:35", "plugin": "core", "name": "start_epoch", "raw_value": "1727031995.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-6", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 6, "time_seconds": 39.706334590911865, "inputs": {"input": {"src": "hda", "id": "f39f4c30dcd74940"}, "addref_cond|addref_select": "no", "cond_region|regions_repeat_0|region": "ref1:10-24", "cond_region|regions_repeat_1|region": "ref1:30-46", "cond_region|regions_repeat_2|region": "ref1:39-56", "cond_region|select_region": "text", "cov_threshold": "4"}, "job": {"model_class": "Job", "id": "f535695a4eeca412", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:58:16.855025", "update_time": "2024-09-22T18:58:31.622154", "galaxy_version": "24.1", "external_id": "gxy-n6wrd", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/5/a/4/dataset_5a434b63-d6d6-4eff-93c8-582d22e6c28d.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/f/f/1/metadata_ff173edb-7e29-422b-a041-64f02ae09caf.dat' infile.bai && samtools stats -g 4 -@ $addthreads infile 'ref1:10-24' 'ref1:30-46' 'ref1:39-56' > '/galaxy/server/database/objects/2/c/5/dataset_2c576097-b550-44ce-9d4c-3e01583e7b9b.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"4\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 1, \"regions_repeat\": [{\"__index__\": 0, \"region\": \"ref1:10-24\"}, {\"__index__\": 1, \"region\": \"ref1:30-46\"}, {\"__index__\": 2, \"region\": \"ref1:39-56\"}], \"select_region\": \"text\"}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "f39f4c30dcd74940", "src": "hda", "uuid": "5a434b63-d6d6-4eff-93c8-582d22e6c28d"}}, "outputs": {"output": {"id": "43cc8889bf9e8f95", "src": "hda", "uuid": "2c576097-b550-44ce-9d4c-3e01583e7b9b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Barcodes with tag BC differ in length at sequence 'ref1_grp1_p002'\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Barcodes with tag BC differ in length at sequence 'ref1_grp1_p002'\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": "2024-09-22 18:58:18", "plugin": "core", "name": "end_epoch", "raw_value": "1727031498.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:58:18", "plugin": "core", "name": "start_epoch", "raw_value": "1727031498.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-6", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 6, "time_seconds": 40.396241664886475, "inputs": {"input": {"src": "hda", "id": "9b4b28f6db17bf6b"}, "addref_cond|addref_select": "no", "cond_region|regions_repeat_0|region": "ref1:10-24", "cond_region|regions_repeat_1|region": "ref1:30-46", "cond_region|regions_repeat_2|region": "ref1:39-56", "cond_region|select_region": "text", "cov_threshold": "4"}, "job": {"model_class": "Job", "id": "31ba71a5468dd219", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:07:13.428211", "update_time": "2024-09-22T19:07:29.072922", "galaxy_version": "24.1", "external_id": "gxy-86tsm", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/2/3/d/dataset_23d0b044-f07e-4634-9f55-e5a075717a3b.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/0/2/e/metadata_02eaa878-8e7f-4838-9817-0e32416be289.dat' infile.bai && samtools stats -g 4 -@ $addthreads infile 'ref1:10-24' 'ref1:30-46' 'ref1:39-56' > '/galaxy/server/database/objects/0/6/c/dataset_06c57085-e54d-4b85-829c-0e31966cefea.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"4\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 1, \"regions_repeat\": [{\"__index__\": 0, \"region\": \"ref1:10-24\"}, {\"__index__\": 1, \"region\": \"ref1:30-46\"}, {\"__index__\": 2, \"region\": \"ref1:39-56\"}], \"select_region\": \"text\"}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "9b4b28f6db17bf6b", "src": "hda", "uuid": "23d0b044-f07e-4634-9f55-e5a075717a3b"}}, "outputs": {"output": {"id": "9d995b72fbfcc507", "src": "hda", "uuid": "06c57085-e54d-4b85-829c-0e31966cefea"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Barcodes with tag BC differ in length at sequence 'ref1_grp1_p002'\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Barcodes with tag BC differ in length at sequence 'ref1_grp1_p002'\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": "2024-09-22 19:07:15", "plugin": "core", "name": "end_epoch", "raw_value": "1727032035.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:07:15", "plugin": "core", "name": "start_epoch", "raw_value": "1727032035.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-7", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 7, "time_seconds": 42.03202176094055, "inputs": {"input": {"src": "hda", "id": "48399b7ba6094602"}, "addref_cond|addref_select": "no", "cond_region|targetregions": {"src": "hda", "id": "916cf8497eadecb5"}, "cond_region|select_region": "tab"}, "job": {"model_class": "Job", "id": "1617b56aab8d2d53", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:58:57.231634", "update_time": "2024-09-22T18:59:13.480635", "galaxy_version": "24.1", "external_id": "gxy-vktn4", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/0/1/5/dataset_015b1b30-a903-4111-adba-4a187412270d.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/d/d/c/metadata_ddc188df-54a1-4a5b-b540-bc69c726b78a.dat' infile.bai && samtools stats -t '/galaxy/server/database/objects/a/6/b/dataset_a6babdd5-ca5e-4938-871e-b6f6376257f2.dat' -@ $addthreads infile > '/galaxy/server/database/objects/3/2/3/dataset_3234bc5c-c303-4478-b338-01afa2f54954.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 2, \"select_region\": \"tab\", \"targetregions\": {\"values\": [{\"id\": 163, \"src\": \"hda\"}]}}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "48399b7ba6094602", "src": "hda", "uuid": "015b1b30-a903-4111-adba-4a187412270d"}, "cond_region|targetregions": {"id": "916cf8497eadecb5", "src": "hda", "uuid": "a6babdd5-ca5e-4938-871e-b6f6376257f2"}}, "outputs": {"output": {"id": "3a1ae83738ad2097", "src": "hda", "uuid": "3234bc5c-c303-4478-b338-01afa2f54954"}}, "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": "2024-09-22 18:58:59", "plugin": "core", "name": "end_epoch", "raw_value": "1727031539.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:58:59", "plugin": "core", "name": "start_epoch", "raw_value": "1727031539.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-7", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 7, "time_seconds": 40.75612187385559, "inputs": {"input": {"src": "hda", "id": "c54c8af4d191f7fb"}, "addref_cond|addref_select": "no", "cond_region|targetregions": {"src": "hda", "id": "6bb6381885f22b6a"}, "cond_region|select_region": "tab"}, "job": {"model_class": "Job", "id": "13cdcdbe98abef25", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:07:54.930398", "update_time": "2024-09-22T19:08:09.850141", "galaxy_version": "24.1", "external_id": "gxy-sj2fc", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/f/f/8/dataset_ff817e41-685e-4375-9002-97a61d3da4cd.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/d/7/b/metadata_d7b27c0a-490e-4543-a55b-339e9010b3d7.dat' infile.bai && samtools stats -t '/galaxy/server/database/objects/a/d/a/dataset_ada9d6ab-4f3f-4180-967d-8821549969bf.dat' -@ $addthreads infile > '/galaxy/server/database/objects/5/b/3/dataset_5b34378e-443d-4a7b-b915-64f8ff6fd9be.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 2, \"select_region\": \"tab\", \"targetregions\": {\"values\": [{\"id\": 202, \"src\": \"hda\"}]}}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "c54c8af4d191f7fb", "src": "hda", "uuid": "ff817e41-685e-4375-9002-97a61d3da4cd"}, "cond_region|targetregions": {"id": "6bb6381885f22b6a", "src": "hda", "uuid": "ada9d6ab-4f3f-4180-967d-8821549969bf"}}, "outputs": {"output": {"id": "66af1366e0051fb7", "src": "hda", "uuid": "5b34378e-443d-4a7b-b915-64f8ff6fd9be"}}, "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": "2024-09-22 19:07:56", "plugin": "core", "name": "end_epoch", "raw_value": "1727032076.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:07:56", "plugin": "core", "name": "start_epoch", "raw_value": "1727032076.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-8", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 8, "time_seconds": 40.52586054801941, "inputs": {"input": {"src": "hda", "id": "3a25d7a20db9a9e7"}, "addref_cond|addref_select": "no", "cond_region|targetregions": {"src": "hda", "id": "6978290ff24c69ad"}, "cond_region|select_region": "tab", "remove_overlaps": true}, "job": {"model_class": "Job", "id": "4c1637f2111138b3", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T18:59:39.100488", "update_time": "2024-09-22T18:59:54.135538", "galaxy_version": "24.1", "external_id": "gxy-7nfjw", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/4/1/2/dataset_412c863c-51b8-41d4-8d89-ed0cbc87ea38.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/7/4/f/metadata_74f6fcd3-f1b2-4bbb-b096-c7e3574208e7.dat' infile.bai && samtools stats -t '/galaxy/server/database/objects/c/3/d/dataset_c3dbea4e-b354-4de6-9524-760c873140ba.dat' -p -@ $addthreads infile > '/galaxy/server/database/objects/0/9/2/dataset_092716c0-64bd-4785-b3db-630d26266489.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "true", "sparse": "false", "cond_region": "{\"__current_case__\": 2, \"select_region\": \"tab\", \"targetregions\": {\"values\": [{\"id\": 166, \"src\": \"hda\"}]}}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "3a25d7a20db9a9e7", "src": "hda", "uuid": "412c863c-51b8-41d4-8d89-ed0cbc87ea38"}, "cond_region|targetregions": {"id": "6978290ff24c69ad", "src": "hda", "uuid": "c3dbea4e-b354-4de6-9524-760c873140ba"}}, "outputs": {"output": {"id": "880a1ea5956edb18", "src": "hda", "uuid": "092716c0-64bd-4785-b3db-630d26266489"}}, "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": "2024-09-22 18:59:40", "plugin": "core", "name": "end_epoch", "raw_value": "1727031580.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 18:59:40", "plugin": "core", "name": "start_epoch", "raw_value": "1727031580.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-8", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 8, "time_seconds": 41.74088168144226, "inputs": {"input": {"src": "hda", "id": "88ce7353c62e31a2"}, "addref_cond|addref_select": "no", "cond_region|targetregions": {"src": "hda", "id": "8964fcf7b6cd4f21"}, "cond_region|select_region": "tab", "remove_overlaps": true}, "job": {"model_class": "Job", "id": "a627cd48f111ee3e", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:08:36.346963", "update_time": "2024-09-22T19:08:51.586694", "galaxy_version": "24.1", "external_id": "gxy-5xn8x", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/6/e/a/dataset_6ea0f978-36cf-488c-8ba4-9e0ac15bea5e.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/6/9/e/metadata_69e8bfed-00d2-4002-a203-91d6f1fe6f55.dat' infile.bai && samtools stats -t '/galaxy/server/database/objects/9/c/0/dataset_9c0c9f13-9ad0-4a63-9912-d82618912a2e.dat' -p -@ $addthreads infile > '/galaxy/server/database/objects/a/e/d/dataset_aed1bc2f-49e9-4207-9fc1-40c12d350526.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "true", "sparse": "false", "cond_region": "{\"__current_case__\": 2, \"select_region\": \"tab\", \"targetregions\": {\"values\": [{\"id\": 205, \"src\": \"hda\"}]}}", "addref_cond": 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"job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-09-22 19:08:37", "plugin": "core", "name": "end_epoch", "raw_value": "1727032117.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:08:37", "plugin": "core", "name": "start_epoch", "raw_value": "1727032117.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-9", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 9, "time_seconds": 42.0452926158905, "inputs": {"input": {"src": "hda", "id": "053bd85423bed0e1"}, "addref_cond|addref_select": "no", "cond_region|targetregions": {"src": "hda", "id": "c930c740de7e1125"}, "cond_region|select_region": "tab"}, "job": {"model_class": "Job", "id": "8e9738d7a25e86a8", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:00:19.811034", "update_time": "2024-09-22T19:00:36.170500", "galaxy_version": "24.1", "external_id": "gxy-tbpwr", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/1/8/0/dataset_1803ce5f-ee7d-44d3-9928-72bc21bc5ef2.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/4/d/d/metadata_4ddf90e2-f60d-42ca-9c84-d5754615453e.dat' infile.bai && samtools stats -t '/galaxy/server/database/objects/3/a/d/dataset_3ad0bd1a-fbc9-494f-9997-6e088fff1373.dat' -@ $addthreads infile > '/galaxy/server/database/objects/8/d/0/dataset_8d04a7ef-5923-425f-8df5-e3b85f86ff10.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 2, \"select_region\": \"tab\", \"targetregions\": {\"values\": [{\"id\": 169, \"src\": \"hda\"}]}}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "053bd85423bed0e1", "src": "hda", "uuid": "1803ce5f-ee7d-44d3-9928-72bc21bc5ef2"}, "cond_region|targetregions": {"id": "c930c740de7e1125", "src": "hda", "uuid": "3ad0bd1a-fbc9-494f-9997-6e088fff1373"}}, "outputs": {"output": {"id": "69d1074d84fd8c41", "src": "hda", "uuid": "8d04a7ef-5923-425f-8df5-e3b85f86ff10"}}, "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": "2024-09-22 19:00:22", "plugin": "core", "name": "end_epoch", "raw_value": "1727031622.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:00:21", "plugin": "core", "name": "start_epoch", "raw_value": "1727031621.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_stats/2.0.5-9", "has_data": true, "data": {"tool_id": "samtools_stats", "tool_version": "2.0.5", "test_index": 9, "time_seconds": 41.03730130195618, "inputs": {"input": {"src": "hda", "id": "0f6be53ba5552638"}, "addref_cond|addref_select": "no", "cond_region|targetregions": {"src": "hda", "id": "8a49f506703cd689"}, "cond_region|select_region": "tab"}, "job": {"model_class": "Job", "id": "67f4878618a03e81", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:09:16.863277", "update_time": "2024-09-22T19:09:32.901110", "galaxy_version": "24.1", "external_id": "gxy-562rv", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/b/6/3/dataset_b63d2068-0314-45cb-8464-7cb3dba6c6f5.dat' infile && ln -s '/galaxy/server/database/objects/_metadata_files/6/5/a/metadata_65a21226-550b-47c8-821f-9042641aff19.dat' infile.bai && samtools stats -t '/galaxy/server/database/objects/0/c/0/dataset_0c0339f7-7bc1-475e-a514-1d940946307c.dat' -@ $addthreads infile > '/galaxy/server/database/objects/9/c/a/dataset_9ca0f14e-a061-4d30-ba04-b73570567cb4.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.20 (using htslib 1.20)", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "cov_threshold": "\"\"", "remove_overlaps": "false", "sparse": "false", "cond_region": "{\"__current_case__\": 2, \"select_region\": \"tab\", \"targetregions\": {\"values\": [{\"id\": 208, \"src\": \"hda\"}]}}", "addref_cond": "{\"__current_case__\": 0, \"addref_select\": \"no\"}", "trim_quality": "\"\"", "most_inserts": "\"\"", "read_length": "\"\"", "read_group": null, "insert_size": "\"\"", "gc_depth": "\"\"", "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}", "split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}", "remove_dups": "false", "coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"}, "inputs": {"input": {"id": "0f6be53ba5552638", "src": "hda", "uuid": "b63d2068-0314-45cb-8464-7cb3dba6c6f5"}, "cond_region|targetregions": {"id": "8a49f506703cd689", "src": "hda", "uuid": "0c0339f7-7bc1-475e-a514-1d940946307c"}}, "outputs": {"output": {"id": "287e2b63bf1cda5c", "src": "hda", "uuid": "9ca0f14e-a061-4d30-ba04-b73570567cb4"}}, "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": 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"tool_version": "1.9.3+galaxy0", "test_index": 0, "time_seconds": 0.1516268253326416, "execution_problem": "Input staging problem: Test input file (louvain_1.0) cannot be found.", "status": "error"}}, {"id": "scanpy_find_markers/1.9.3+galaxy0-1", "has_data": true, "data": {"tool_id": "scanpy_find_markers", "tool_version": "1.9.3+galaxy0", "test_index": 1, "time_seconds": 0.11040520668029785, "execution_problem": "Input staging problem: Test input file (louvain_1.0) cannot be found.", "status": "error"}}, {"id": "scanpy_find_markers/1.9.3+galaxy0-1", "has_data": true, "data": {"tool_id": "scanpy_find_markers", "tool_version": "1.9.3+galaxy0", "test_index": 1, "time_seconds": 0.11226630210876465, "execution_problem": "Input staging problem: Test input file (louvain_1.0) cannot be found.", "status": "error"}}, {"id": "scanpy_find_markers/1.9.3+galaxy0-2", "has_data": true, "data": {"tool_id": "scanpy_find_markers", "tool_version": "1.9.3+galaxy0", "test_index": 2, "time_seconds": 0.11058378219604492, "execution_problem": "Input staging problem: Test input file (mnn.h5) cannot be found.", "status": "error"}}, {"id": "scanpy_find_markers/1.9.3+galaxy0-2", "has_data": true, "data": {"tool_id": "scanpy_find_markers", "tool_version": "1.9.3+galaxy0", "test_index": 2, "time_seconds": 0.10867762565612793, "execution_problem": "Input staging problem: Test input file (mnn.h5) cannot be found.", "status": "error"}}, {"id": "scater_filter/1.22.0-0", "has_data": true, "data": {"tool_id": "scater_filter", "tool_version": "1.22.0", "test_index": 0, "time_seconds": 78.72358846664429, "inputs": {"input_loom": {"src": "hda", "id": "f9c7d80def2075e6"}, "filter_type|library_size": "100000", "filter_type|percent_counts_MT": "33.0", "filter_type|detection_limit": "4", "filter_type|min_cells_expressed": "3", "filter_type|filter_type_selector": "manual"}, "job": {"model_class": "Job", "id": "1280ceb1907d7cfb", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:21:42.409572", "update_time": "2024-09-22T19:22:38.190717", "galaxy_version": "24.1", "external_id": "gxy-jdn4b", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/652923ce664f/scater_filter/scater-manual-filter.R' -i '/galaxy/server/database/objects/7/e/d/dataset_7ed66202-8143-48cc-97ea-aece67ea946b.dat' --library-size 100000 --percent-counts-MT 33.0 --expressed-features 100 --detection-limit 4.0 --min-cells-expressed 3 -o '/galaxy/server/database/objects/d/c/1/dataset_dc1da02e-42bc-434c-92c1-cf15f3d75413.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_type": "{\"__current_case__\": 0, \"detection_limit\": \"4.0\", \"expressed_features\": \"100\", \"filter_type_selector\": \"manual\", \"library_size\": \"100000\", \"min_cells_expressed\": \"3\", \"percent_counts_MT\": \"33.0\"}"}, "inputs": {"input_loom": {"id": "f9c7d80def2075e6", "src": "hda", "uuid": "7ed66202-8143-48cc-97ea-aece67ea946b"}}, "outputs": {"output_loom": {"id": "6c14be0d53f56c3a", "src": "hda", "uuid": "dc1da02e-42bc-434c-92c1-cf15f3d75413"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[1] \"Starting with 40 cells and 2000 features.\"\n[1] \"After filtering out low library counts: 39 cells and 2000 features.\"\n[1] \"After filtering out high MT gene counts: 34 cells and 2000 features.\"\n[1] \"After filtering out cells with low feature counts: 34 cells and 2000 features.\"\n[1] \"After filtering out rare features: 34 cells and 1148 features.\"\n[1] TRUE\n", "tool_stderr": "Loading required package: S4Vectors\nLoading required package: stats4\nLoading required package: BiocGenerics\n\nAttaching package: \u2018BiocGenerics\u2019\n\nThe following objects are masked from \u2018package:stats\u2019:\n\n IQR, mad, sd, var, xtabs\n\nThe following objects are masked from \u2018package:base\u2019:\n\n anyDuplicated, append, as.data.frame, basename, cbind, colnames,\n dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,\n grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,\n order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\n rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,\n union, unique, unsplit, which.max, which.min\n\n\nAttaching package: \u2018S4Vectors\u2019\n\nThe following objects are masked from \u2018package:base\u2019:\n\n expand.grid, I, unname\n\nLoading required package: SingleCellExperiment\nLoading required package: SummarizedExperiment\nLoading required package: MatrixGenerics\nLoading required package: matrixStats\n\nAttaching package: \u2018MatrixGenerics\u2019\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,\n colCounts, colCummaxs, colCummins, colCumprods, colCumsums,\n colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,\n colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,\n colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,\n colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,\n colWeightedMeans, colWeightedMedians, colWeightedSds,\n colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,\n rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,\n rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,\n rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,\n rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,\n rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,\n rowWeightedMads, rowWeightedMeans, rowWeightedMedians,\n rowWeightedSds, rowWeightedVars\n\nLoading required package: GenomicRanges\nLoading required package: IRanges\nLoading required package: GenomeInfoDb\nLoading required package: Biobase\nWelcome to Bioconductor\n\n Vignettes contain introductory material; view with\n 'browseVignettes()'. To cite Bioconductor, see\n 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\n\nAttaching package: \u2018Biobase\u2019\n\nThe following object is masked from \u2018package:MatrixGenerics\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n anyMissing, rowMedians\n\nLoading required package: rhdf5\nLoading required package: BiocIO\nLoading required package: scuttle\nLoading required package: ggplot2\nWarning message:\nIn value[[3L]](cond) :\n zero-length inputs cannot be mixed with those of non-zero length\n", "job_stdout": "", "job_stderr": "", "stdout": "[1] \"Starting with 40 cells and 2000 features.\"\n[1] \"After filtering out low library counts: 39 cells and 2000 features.\"\n[1] \"After filtering out high MT gene counts: 34 cells and 2000 features.\"\n[1] \"After filtering out cells with low feature counts: 34 cells and 2000 features.\"\n[1] \"After filtering out rare features: 34 cells and 1148 features.\"\n[1] TRUE\n", "stderr": "Loading required package: S4Vectors\nLoading required package: stats4\nLoading required package: BiocGenerics\n\nAttaching package: \u2018BiocGenerics\u2019\n\nThe following objects are masked from \u2018package:stats\u2019:\n\n IQR, mad, sd, var, xtabs\n\nThe following objects are masked from \u2018package:base\u2019:\n\n anyDuplicated, append, as.data.frame, basename, cbind, colnames,\n dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,\n grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,\n order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\n rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,\n union, unique, unsplit, which.max, which.min\n\n\nAttaching package: \u2018S4Vectors\u2019\n\nThe following objects are masked from \u2018package:base\u2019:\n\n expand.grid, I, unname\n\nLoading required package: SingleCellExperiment\nLoading required package: SummarizedExperiment\nLoading required package: MatrixGenerics\nLoading required package: matrixStats\n\nAttaching package: \u2018MatrixGenerics\u2019\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,\n colCounts, colCummaxs, colCummins, colCumprods, colCumsums,\n colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,\n colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,\n colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,\n colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,\n colWeightedMeans, colWeightedMedians, colWeightedSds,\n colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,\n rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,\n rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,\n rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,\n rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,\n rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,\n rowWeightedMads, rowWeightedMeans, rowWeightedMedians,\n rowWeightedSds, rowWeightedVars\n\nLoading required package: GenomicRanges\nLoading required package: IRanges\nLoading required package: GenomeInfoDb\nLoading required package: Biobase\nWelcome to Bioconductor\n\n Vignettes contain introductory material; view with\n 'browseVignettes()'. To cite Bioconductor, see\n 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\n\nAttaching package: \u2018Biobase\u2019\n\nThe following object is masked from \u2018package:MatrixGenerics\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n anyMissing, rowMedians\n\nLoading required package: rhdf5\nLoading required package: BiocIO\nLoading required package: scuttle\nLoading required package: ggplot2\nWarning message:\nIn value[[3L]](cond) :\n zero-length inputs cannot be mixed with those of non-zero length\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": "2024-09-22 19:22:18", "plugin": "core", "name": "end_epoch", "raw_value": "1727032938.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:22:05", "plugin": "core", "name": "start_epoch", "raw_value": "1727032925.0000000"}, {"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": "scater_filter/1.22.0-0", "has_data": true, "data": {"tool_id": "scater_filter", "tool_version": "1.22.0", "test_index": 0, "time_seconds": 49.10424447059631, "inputs": {"input_loom": {"src": "hda", "id": "bcf67f71eb2f1104"}, "filter_type|library_size": "100000", "filter_type|percent_counts_MT": "33.0", "filter_type|detection_limit": "4", "filter_type|min_cells_expressed": "3", "filter_type|filter_type_selector": "manual"}, "job": {"model_class": "Job", "id": "e4fe8429e6deaecc", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:23:53.471769", "update_time": "2024-09-22T19:24:20.356301", "galaxy_version": "24.1", "external_id": "gxy-z7x8c", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/652923ce664f/scater_filter/scater-manual-filter.R' -i '/galaxy/server/database/objects/5/8/2/dataset_582a5007-4558-45a6-8dab-d4981675b881.dat' --library-size 100000 --percent-counts-MT 33.0 --expressed-features 100 --detection-limit 4.0 --min-cells-expressed 3 -o '/galaxy/server/database/objects/0/f/3/dataset_0f3c8bea-a022-43cc-af7d-906c5992f1b7.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_type": "{\"__current_case__\": 0, \"detection_limit\": \"4.0\", \"expressed_features\": \"100\", \"filter_type_selector\": \"manual\", \"library_size\": \"100000\", \"min_cells_expressed\": \"3\", \"percent_counts_MT\": \"33.0\"}"}, "inputs": {"input_loom": {"id": "bcf67f71eb2f1104", "src": "hda", "uuid": "582a5007-4558-45a6-8dab-d4981675b881"}}, "outputs": {"output_loom": {"id": "0a2c7dbe51c6b803", "src": "hda", "uuid": "0f3c8bea-a022-43cc-af7d-906c5992f1b7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[1] \"Starting with 40 cells and 2000 features.\"\n[1] \"After filtering out low library counts: 39 cells and 2000 features.\"\n[1] \"After filtering out high MT gene counts: 34 cells and 2000 features.\"\n[1] \"After filtering out cells with low feature counts: 34 cells and 2000 features.\"\n[1] \"After filtering out rare features: 34 cells and 1148 features.\"\n[1] TRUE\n", "tool_stderr": "Loading required package: S4Vectors\nLoading required package: stats4\nLoading required package: BiocGenerics\n\nAttaching package: \u2018BiocGenerics\u2019\n\nThe following objects are masked from \u2018package:stats\u2019:\n\n IQR, mad, sd, var, xtabs\n\nThe following objects are masked from \u2018package:base\u2019:\n\n anyDuplicated, append, as.data.frame, basename, cbind, colnames,\n dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,\n grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,\n order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\n rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,\n union, unique, unsplit, which.max, which.min\n\n\nAttaching package: \u2018S4Vectors\u2019\n\nThe following objects are masked from \u2018package:base\u2019:\n\n expand.grid, I, unname\n\nLoading required package: SingleCellExperiment\nLoading required package: SummarizedExperiment\nLoading required package: MatrixGenerics\nLoading required package: matrixStats\n\nAttaching package: \u2018MatrixGenerics\u2019\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,\n colCounts, colCummaxs, colCummins, colCumprods, colCumsums,\n colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,\n colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,\n colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,\n colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,\n colWeightedMeans, colWeightedMedians, colWeightedSds,\n colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,\n rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,\n rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,\n rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,\n rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,\n rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,\n rowWeightedMads, rowWeightedMeans, rowWeightedMedians,\n rowWeightedSds, rowWeightedVars\n\nLoading required package: GenomicRanges\nLoading required package: IRanges\nLoading required package: GenomeInfoDb\nLoading required package: Biobase\nWelcome to Bioconductor\n\n Vignettes contain introductory material; view with\n 'browseVignettes()'. To cite Bioconductor, see\n 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\n\nAttaching package: \u2018Biobase\u2019\n\nThe following object is masked from \u2018package:MatrixGenerics\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n anyMissing, rowMedians\n\nLoading required package: rhdf5\nLoading required package: BiocIO\nLoading required package: scuttle\nLoading required package: ggplot2\nWarning message:\nIn value[[3L]](cond) :\n zero-length inputs cannot be mixed with those of non-zero length\n", "job_stdout": "", "job_stderr": "", "stdout": "[1] \"Starting with 40 cells and 2000 features.\"\n[1] \"After filtering out low library counts: 39 cells and 2000 features.\"\n[1] \"After filtering out high MT gene counts: 34 cells and 2000 features.\"\n[1] \"After filtering out cells with low feature counts: 34 cells and 2000 features.\"\n[1] \"After filtering out rare features: 34 cells and 1148 features.\"\n[1] TRUE\n", "stderr": "Loading required package: S4Vectors\nLoading required package: stats4\nLoading required package: BiocGenerics\n\nAttaching package: \u2018BiocGenerics\u2019\n\nThe following objects are masked from \u2018package:stats\u2019:\n\n IQR, mad, sd, var, xtabs\n\nThe following objects are masked from \u2018package:base\u2019:\n\n anyDuplicated, append, as.data.frame, basename, cbind, colnames,\n dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,\n grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,\n order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\n rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,\n union, unique, unsplit, which.max, which.min\n\n\nAttaching package: \u2018S4Vectors\u2019\n\nThe following objects are masked from \u2018package:base\u2019:\n\n expand.grid, I, unname\n\nLoading required package: SingleCellExperiment\nLoading required package: SummarizedExperiment\nLoading required package: MatrixGenerics\nLoading required package: matrixStats\n\nAttaching package: \u2018MatrixGenerics\u2019\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,\n colCounts, colCummaxs, colCummins, colCumprods, colCumsums,\n colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,\n colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,\n colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,\n colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,\n colWeightedMeans, colWeightedMedians, colWeightedSds,\n colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,\n rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,\n rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,\n rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,\n rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,\n rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,\n rowWeightedMads, rowWeightedMeans, rowWeightedMedians,\n rowWeightedSds, rowWeightedVars\n\nLoading required package: GenomicRanges\nLoading required package: IRanges\nLoading required package: GenomeInfoDb\nLoading required package: Biobase\nWelcome to Bioconductor\n\n Vignettes contain introductory material; view with\n 'browseVignettes()'. To cite Bioconductor, see\n 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\n\nAttaching package: \u2018Biobase\u2019\n\nThe following object is masked from \u2018package:MatrixGenerics\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n anyMissing, rowMedians\n\nLoading required package: rhdf5\nLoading required package: BiocIO\nLoading required package: scuttle\nLoading required package: ggplot2\nWarning message:\nIn value[[3L]](cond) :\n zero-length inputs cannot be mixed with those of non-zero length\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": "2024-09-22 19:24:07", "plugin": "core", "name": "end_epoch", "raw_value": "1727033047.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:23:54", "plugin": "core", "name": "start_epoch", "raw_value": "1727033034.0000000"}, {"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": "scater_filter/1.22.0-1", "has_data": true, "data": {"tool_id": "scater_filter", "tool_version": "1.22.0", "test_index": 1, "time_seconds": 51.92537879943848, "inputs": {"input_loom": {"src": "hda", "id": "a25a9e50d2b08fd4"}, "filter_type|filter_type_selector": "pca"}, "job": {"model_class": "Job", "id": "412f6bf3e98cc878", "history_id": "b2116f9eb07476cf", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.22.0", "state": "ok", "exit_code": 0, "create_time": "2024-09-22T19:23:01.810863", "update_time": "2024-09-22T19:23:30.217522", "galaxy_version": "24.1", "external_id": "gxy-wq9cs", "handler": null, "job_runner_name": null, "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/652923ce664f/scater_filter/scater-pca-filter.R' -i '/galaxy/server/database/objects/d/7/4/dataset_d74081d1-2bf0-41ac-bf4b-6f3e23d6e835.dat' -o '/galaxy/server/database/objects/5/1/a/dataset_51af3c22-d57a-4c7c-9289-d52a7700bead.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "filter_type": "{\"__current_case__\": 1, \"filter_type_selector\": \"pca\"}"}, "inputs": {"input_loom": {"id": "a25a9e50d2b08fd4", "src": "hda", "uuid": "d74081d1-2bf0-41ac-bf4b-6f3e23d6e835"}}, "outputs": {"output_loom": {"id": "fc45d9188152efcf", "src": "hda", "uuid": "51af3c22-d57a-4c7c-9289-d52a7700bead"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[1] \"Starting with 40 cells\"\n[1] \"Ending with 33 cells\"\n[1] TRUE\n", "tool_stderr": "Loading required package: S4Vectors\nLoading required package: stats4\nLoading required package: BiocGenerics\n\nAttaching package: \u2018BiocGenerics\u2019\n\nThe following objects are masked from \u2018package:stats\u2019:\n\n IQR, mad, sd, var, xtabs\n\nThe following objects are masked from \u2018package:base\u2019:\n\n anyDuplicated, append, as.data.frame, basename, cbind, colnames,\n dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,\n grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,\n order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\n rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,\n union, unique, unsplit, which.max, which.min\n\n\nAttaching package: \u2018S4Vectors\u2019\n\nThe following objects are masked from \u2018package:base\u2019:\n\n expand.grid, I, unname\n\nLoading required package: SingleCellExperiment\nLoading required package: SummarizedExperiment\nLoading required package: MatrixGenerics\nLoading required package: matrixStats\n\nAttaching package: \u2018MatrixGenerics\u2019\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,\n colCounts, colCummaxs, colCummins, colCumprods, colCumsums,\n colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,\n colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,\n colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,\n colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,\n colWeightedMeans, colWeightedMedians, colWeightedSds,\n colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,\n rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,\n rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,\n rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,\n rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,\n rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,\n rowWeightedMads, rowWeightedMeans, rowWeightedMedians,\n rowWeightedSds, rowWeightedVars\n\nLoading required package: GenomicRanges\nLoading required package: IRanges\nLoading required package: GenomeInfoDb\nLoading required package: Biobase\nWelcome to Bioconductor\n\n Vignettes contain introductory material; view with\n 'browseVignettes()'. To cite Bioconductor, see\n 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\n\nAttaching package: \u2018Biobase\u2019\n\nThe following object is masked from \u2018package:MatrixGenerics\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n anyMissing, rowMedians\n\nLoading required package: rhdf5\nLoading required package: BiocIO\nLoading required package: scuttle\nLoading required package: ggplot2\n\nAttaching package: \u2018robustbase\u2019\n\nThe following object is masked from \u2018package:Biobase\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:MatrixGenerics\u2019:\n\n colMedians, rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n colMedians, rowMedians\n\n", "job_stdout": "", "job_stderr": "", "stdout": "[1] \"Starting with 40 cells\"\n[1] \"Ending with 33 cells\"\n[1] TRUE\n", "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\n\nAttaching package: \u2018robustbase\u2019\n\nThe following object is masked from \u2018package:Biobase\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:MatrixGenerics\u2019:\n\n colMedians, rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n colMedians, rowMedians\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "12 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "12.0000000"}, 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\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 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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\n\nAttaching package: \u2018robustbase\u2019\n\nThe following object is masked from \u2018package:Biobase\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:MatrixGenerics\u2019:\n\n colMedians, rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n colMedians, rowMedians\n\n", "job_stdout": "", "job_stderr": "", "stdout": "[1] \"Starting with 40 cells\"\n[1] \"Ending with 33 cells\"\n[1] TRUE\n", "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\n\nAttaching package: \u2018robustbase\u2019\n\nThe following object is masked from \u2018package:Biobase\u2019:\n\n rowMedians\n\nThe following objects are masked from \u2018package:MatrixGenerics\u2019:\n\n colMedians, rowMedians\n\nThe following objects are masked from \u2018package:matrixStats\u2019:\n\n colMedians, rowMedians\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "12 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "12.0000000"}, 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"uuid": "363fc9e3-e42b-46ce-aad7-ab8de12869ee"}}, "outputs": {"out_file1": {"id": "b5505ec844970eb3", "src": "hda", "uuid": "b8c34f2d-bc42-4121-a66a-0278e51ca199"}}, "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": "2024-09-22 19:32:33", "plugin": "core", "name": "end_epoch", "raw_value": "1727033553.0000000"}, {"title": "Job Start Time", "value": "2024-09-22 19:32:32", "plugin": "core", "name": "start_epoch", "raw_value": "1727033552.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}], "galaxy_url": "http://35.237.74.68:8000/galaxy/"} \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/results.xunit b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/results.xunit new file mode 100644 index 000000000..0f3b84ae7 --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/results.xunit @@ -0,0 +1,1080 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -> print.numeric_version -> print -> print.defaultExecution haltedCells: 1025 + ]]> + + + + + + + + -> print.numeric_version -> print -> print.defaultExecution haltedCells: 1025 + ]]> + + + + + + + + -> print.numeric_version -> print -> print.defaultExecution haltedCells: 1025 + ]]> + + + + + + + + + + + + + + -> print.numeric_version -> print -> print.defaultExecution haltedWarning message:In xy.coords(x, y, xlabel, ylabel, log) : 7432 y values <= 0 omitted from logarithmic plot + ]]> + + + + + + + + + + -> print.numeric_version -> print -> print.defaultExecution haltedWarning message:In xy.coords(x, y, xlabel, ylabel, log) : 7432 y values <= 0 omitted from logarithmic plot + ]]> + + + + + + + + -> print.numeric_version -> print -> print.defaultExecution haltedCells: 998Cells and Limited: 998 + ]]> + + + + + + + + + + + + + + + + -> print.numeric_version -> print -> print.defaultExecution haltedCells: 954Cells and Limited: 85 + ]]> + + + + + + + + -> print.numeric_version -> print -> print.defaultExecution haltedCells: 954Cells and Limited: 85 + ]]> + + + + + + + + -> print.numeric_version -> print -> print.defaultExecution haltedCells: 2650 + ]]> + + + + + + + + -> print.numeric_version -> print -> print.defaultExecution haltedCells: 2650 + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')() File "/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py", line 543, in main args.func(parser, args) File "/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py", line 55, in run_subtool submodule.run(parser, args) File "/usr/local/lib/python2.7/site-packages/poretools/events.py", line 17, in run for fast5 in Fast5File.Fast5FileSet(args.files): File "/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py", line 110, in next shutil.rmtree(PORETOOLS_TMPDIR) File "/usr/local/lib/python2.7/shutil.py", line 261, in rmtree rmtree(fullname, ignore_errors, onerror) File "/usr/local/lib/python2.7/shutil.py", line 270, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/usr/local/lib/python2.7/shutil.py", line 268, in rmtree os.rmdir(path)OSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data' + ]]> + + + + + + + + + + load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')() File "/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py", line 543, in main args.func(parser, args) File "/usr/local/lib/python2.7/site-packages/poretools/poretools_main.py", line 55, in run_subtool submodule.run(parser, args) File "/usr/local/lib/python2.7/site-packages/poretools/events.py", line 13, in run for fast5 in Fast5File.Fast5FileSet(args.files): File "/usr/local/lib/python2.7/site-packages/poretools/Fast5File.py", line 110, in next shutil.rmtree(PORETOOLS_TMPDIR) File "/usr/local/lib/python2.7/shutil.py", line 261, in rmtree rmtree(fullname, ignore_errors, onerror) File "/usr/local/lib/python2.7/shutil.py", line 270, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/usr/local/lib/python2.7/shutil.py", line 268, in rmtree os.rmdir(path)OSError: [Errno 39] Directory not empty: '.poretools_tmp/test-data' + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/tools.yml b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/tools.yml new file mode 100644 index 000000000..3c0757afc --- /dev/null +++ b/reports/anvil-edge/tool-tests/edge-24-09-22-18-15-1/tools.yml @@ -0,0 +1,122 @@ +chunk: 13 +tools: +- name: deeptools_plot_heatmap + owner: bgruening + revisions: + - a4dfb122e52b + tool_panel_section_id: deeptools + tool_panel_section_label: deepTools +- name: deeptools_plot_profile + owner: bgruening + revisions: + - c361b12d207a + tool_panel_section_id: deeptools + tool_panel_section_label: deepTools +- name: fastp + owner: iuc + revisions: + - dbf9c561ef29 + tool_panel_section_id: fastq_quality_control + tool_panel_section_label: FASTQ Quality Control +- name: rgrnastar + owner: iuc + revisions: + - c772497b2c32 + - 2055c2667eb3 + - 980d2a2e1180 + tool_panel_section_id: mapping + tool_panel_section_label: Mapping +- name: poretools_events + owner: iuc + revisions: + - 28d7819c312f + tool_panel_section_id: nanopore + tool_panel_section_label: Nanopore +- name: pharmcat + owner: bgruening + revisions: + - d67642a21a1d + tool_panel_section_id: pharmacology + tool_panel_section_label: Pharmacology +- name: qualimap_bamqc + owner: iuc + revisions: + - 19ece8afbaab + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: samtools_stats + owner: devteam + revisions: + - 145f6d74ff5e + - 24c5d43cb545 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: filter_on_md + owner: boris + revisions: + - ac70bfaf1224 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: dropletutils + owner: iuc + revisions: + - a9caad671439 + - 2c1200fba922 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scater_filter + owner: iuc + revisions: + - 652923ce664f + - b7ea9f09c02f + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: sceasy_convert + owner: ebi-gxa + revisions: + - f62bc418173f + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_find_markers + owner: ebi-gxa + revisions: + - eb01a7e59e9a + - f04dd4e5b6a7 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: reshape2_cast + owner: iuc + revisions: + - d3b66a3a08ca + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: snpsift_genesets + owner: iuc + revisions: + - d12a810c837e + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: bcftools_plugin_setgt + owner: iuc + revisions: + - 8abfcd1a6949 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: bcftools_call + owner: iuc + revisions: + - 072f606e2e69 + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: vcfbreakcreatemulti + owner: devteam + revisions: + - 9fd5d91eb91b + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF +- name: vcfselectsamples + owner: devteam + revisions: + - 2ba3b87f904f + tool_panel_section_id: vcf_bcf + tool_panel_section_label: VCF/BCF